I created a small example project to show two problems I'm experiencing in the configuration of Spring Boot validation and its integration with Hibernate. I already tried other replies I found about the topic but unfortunately they didn't work for me or that asked to disable Hibernate validation.
I want use a custom Validator implementing ConstraintValidator<ValidUser, User> and inject in it my UserRepository.
At the same time I want to keep the default behaviour of Hibernate that checks for validation errors during update/persist.
I write here for completeness main sections of the app.
Custom configuration
In this class I set a custom validator with a custom MessageSource, so Spring will read messages from the file resources/messages.properties
@Configuration
public class CustomConfiguration {
    @Bean
    public MessageSource messageSource() {
        ReloadableResourceBundleMessageSource messageSource = new ReloadableResourceBundleMessageSource();
        messageSource.setBasenames("classpath:/messages");
        messageSource.setUseCodeAsDefaultMessage(false);
        messageSource.setCacheSeconds((int) TimeUnit.HOURS.toSeconds(1));
        messageSource.setFallbackToSystemLocale(false);
        return messageSource;
    }
    @Bean
    public LocalValidatorFactoryBean validator() {
        LocalValidatorFactoryBean factoryBean = new LocalValidatorFactoryBean();
        factoryBean.setValidationMessageSource(messageSource());
        return factoryBean;
    }
    @Bean
    public MethodValidationPostProcessor methodValidationPostProcessor() {
        MethodValidationPostProcessor methodValidationPostProcessor = new MethodValidationPostProcessor();
        methodValidationPostProcessor.setValidator(validator());
        return methodValidationPostProcessor;
    }
}
The bean
Nothing special here if not the custom validator @ValidUser
@ValidUser
@Entity
public class User extends AbstractPersistable<Long> {
    private static final long serialVersionUID = 1119004705847418599L;
    @NotBlank
    @Column(nullable = false)
    private String name;
    /** CONTACT INFORMATION **/
    @Pattern(regexp = "^\\+{1}[1-9]\\d{1,14}$")
    private String landlinePhone;
    @Pattern(regexp = "^\\+{1}[1-9]\\d{1,14}$")
    private String mobilePhone;
    @NotBlank
    @Column(nullable = false, unique = true)
    private String username;
    @Email
    private String email;
    @JsonIgnore
    private String password;
    @Min(value = 0)
    private BigDecimal cashFund = BigDecimal.ZERO;
    public User() {
    }
    public String getName() {
        return name;
    }
    public void setName(String name) {
        this.name = name;
    }
    public String getLandlinePhone() {
        return landlinePhone;
    }
    public void setLandlinePhone(String landlinePhone) {
        this.landlinePhone = landlinePhone;
    }
    public String getMobilePhone() {
        return mobilePhone;
    }
    public void setMobilePhone(String mobilePhone) {
        this.mobilePhone = mobilePhone;
    }
    public String getUsername() {
        return username;
    }
    public void setUsername(String username) {
        this.username = username;
    }
    public String getEmail() {
        return email;
    }
    public void setEmail(String email) {
        this.email = email;
    }
    public String getPassword() {
        return password;
    }
    public void setPassword(String password) {
        this.password = password;
    }
    public BigDecimal getCashFund() {
        return cashFund;
    }
    public void setCashFund(BigDecimal cashFund) {
        this.cashFund = cashFund;
    }
}
Custom validator Here is where I try to inject the repository. The repository is always null if not when I disable Hibernate validation.
    public class UserValidator implements ConstraintValidator<ValidUser, User> {
    private Logger log = LogManager.getLogger();
    @Autowired
    private UserRepository userRepository;
    @Override
    public void initialize(ValidUser constraintAnnotation) {
    }
    @Override
    public boolean isValid(User value, ConstraintValidatorContext context) {
        try {
            User foundUser = userRepository.findByUsername(value.getUsername());
            if (foundUser != null && foundUser.getId() != value.getId()) {
                context.disableDefaultConstraintViolation();
                context.buildConstraintViolationWithTemplate("{ValidUser.unique.username}").addConstraintViolation();
                return false;
            }
        } catch (Exception e) {
            log.error("", e);
            return false;
        }
        return true;
    }
}
messages.properties
#CUSTOM VALIDATORS
ValidUser.message = I dati inseriti non sono validi. Verificare nuovamente e ripetere l'operazione.
ValidUser.unique.username = L'username [${validatedValue.getUsername()}] è già stato utilizzato. Sceglierne un altro e ripetere l'operazione.
#DEFAULT VALIDATORS
org.hibernate.validator.constraints.NotBlank.message = Il campo non può essere vuoto
# === USER ===
Pattern.user.landlinePhone = Il numero di telefono non è valido. Dovrebbe essere nel formato E.123 internazionale (https://en.wikipedia.org/wiki/E.123)
In my tests, you can try from the source code, I've two problems:
- The injected repository inside 
UserValidatoris null if I don't disable Hibernate validation (spring.jpa.properties.javax.persistence.validation.mode=none) - Even if I disable Hibernate validator, my test cases fail because something prevent Spring to use the default string interpolation for validation messages that should be something like [Constraint].[class name lowercase].[propertyName]. I don't want to use the constraint annotation with the value element like this 
@NotBlank(message="{mycustom.message}")because I don't see the point considering that has his own convetion for interpolation and I can take advantage of that...that means less coding. 
I attach the code; you can just run Junit tests and see errors (Hibernate validation is enable, check application.properties).
What am I doing wrong? What could I do to solve those two problems?
====== UPDATE ======
Just to clarify, reading Spring validation documentation https://docs.spring.io/spring/docs/current/spring-framework-reference/core.html#validation-beanvalidation-spring-constraints they say:
By default, the LocalValidatorFactoryBean configures a SpringConstraintValidatorFactory that uses Spring to create ConstraintValidator instances. This allows your custom ConstraintValidators to benefit from dependency injection like any other Spring bean.
As you can see, a ConstraintValidator implementation may have its dependencies @Autowired like any other Spring bean.
In my configuration class I created my LocalValidatorFactoryBean as they write.
Another interesting questions are this and this, but I had not luck with them.
====== UPDATE 2 ======
After a lot of reseach, seems with Hibernate validator the injection is not provided.
I found a couple of way you can do that:
1st way
Create this configuration class:
 @Configuration
public class HibernateValidationConfiguration extends HibernateJpaAutoConfiguration {
    public HibernateValidationConfiguration(DataSource dataSource, JpaProperties jpaProperties,
            ObjectProvider<JtaTransactionManager> jtaTransactionManager,
            ObjectProvider<TransactionManagerCustomizers> transactionManagerCustomizers) {
        super(dataSource, jpaProperties, jtaTransactionManager, transactionManagerCustomizers);
    }
    @Autowired
    private Validator validator;
    @Override
    protected void customizeVendorProperties(Map<String, Object> vendorProperties) {
        super.customizeVendorProperties(vendorProperties);
        vendorProperties.put("javax.persistence.validation.factory", validator);
    }
}
2nd way
Create an utility bean
    @Service
public class BeanUtil implements ApplicationContextAware {
    private static ApplicationContext context;
    @Override
    public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
        context = applicationContext;
    }
    public static <T> T getBean(Class<T> beanClass) {
        return context.getBean(beanClass);
    }
}
and then in the validator initialization:
@Override
 public void initialize(ValidUser constraintAnnotation) {
 userRepository = BeanUtil.getBean(UserRepository.class);
 em = BeanUtil.getBean(EntityManager.class);
 }
very important
In both cases, in order to make the it works you have to "reset" the entity manager in this way:
@Override
public boolean isValid(User value, ConstraintValidatorContext context) {
    try {
        em.setFlushMode(FlushModeType.COMMIT);
        //your code
    } finally {
        em.setFlushMode(FlushModeType.AUTO);
    }
}
Anyway, I don't know if this is really a safe way. Probably it's not a good practice access to the persistence layer at all.