I guess I managed to do what you asked.
dir/App.java
import java.util.Comparator;
public class App {
    public static void main(String[] args) {
        foo1(new Comparator<Integer>() {
            @Override
            public int compare(Integer o1, Integer o2) {
                return 0;
            }
        });
        foo2(new Comparator<String>() {
            @Override
            public int compare(String o1, String o2) {
                return 0;
            }
        });
    }
}
src/main/java/MyProcessor.java
import spoon.Launcher;
import spoon.processing.AbstractProcessor;
import spoon.reflect.declaration.CtClass;
import spoon.reflect.declaration.CtMethod;
import spoon.reflect.declaration.CtType;
import spoon.reflect.visitor.filter.AbstractFilter;
import spoon.support.compiler.FileSystemFile;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.Collection;
import java.util.List;
public class MyProcessor extends AbstractProcessor<CtType<?>> {
    @Override
    public boolean isToBeProcessed(CtType<?> candidate) {
        if (candidate instanceof CtClass<?> && ((CtClass<?>) candidate).isAnonymous() == true) {
            CtClass<?> clas = (CtClass<?>) candidate;
            List<CtMethod<?>> list = clas.filterChildren(
                    new AbstractFilter<CtMethod<?>>(CtMethod.class) {
                        @Override
                        public boolean matches(CtMethod<?> method) {
                            return method.getSimpleName().equals("compare");
                        }
                    }
            ).list();
            return !(list == null || list.isEmpty());
        }
        return false;
    }
    @Override
    public void process(CtType<?> element) {
        String implementsString = element.getParent().toString()
                .replace("()", "")
                .replace("new", "implements");
        String codeA =
                "public class A {\n" +
                "  public void m() {\n" +
                "    Main.testComparator(new B());\n" +
                "  }\n" +
                "}";
        String codeB = "public class B " + implementsString;
        String fileNameA = "dir2/A.java";
        String fileNameB = "dir2/B.java";
        try (FileWriter fileWriterA = new FileWriter(fileNameA);
             FileWriter fileWriterB = new FileWriter(fileNameB)) {
            fileWriterA.write(codeA);
            fileWriterB.write(codeB);
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
        Launcher launcher = new Launcher();
        launcher.addInputResource("dir2");
        Collection<CtType<?>> allTypes = launcher.buildModel().getAllTypes();
        CtClass<?> ctClassA = (CtClass<?>) allTypes.stream().findFirst().get();
        Object instance = ctClassA.newInstance();
        Class<?> classA = instance.getClass();
        try {
            Method method = classA.getMethod("m");
            method.invoke(instance);
        } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException e) {
            throw new RuntimeException(e);
        }
    }
}
src/main/java/Main.java
import spoon.Launcher;
import java.util.Comparator;
public class Main {
    public static void testComparator(Comparator<?> comparator) {
        System.out.println("test Comparator");
    }
    public static void main(String[] args) {
        Launcher launcher = new Launcher();
        launcher.addInputResource("dir");
        launcher.addProcessor(new MyProcessor());
        launcher.run();
    }
}
dir2/A.java
dir2/B.java
pom.xml
...
<dependency>
    <groupId>fr.inria.gforge.spoon</groupId>
    <artifactId>spoon-core</artifactId>
    <version>8.2.0</version>
</dependency>
Also directory spooned-classes has to be added to classpath. I'm using sbt. This can be specified there as unmanagedClasspath in Runtime ++= Seq(file("spooned-classes")).classpath. In Maven this should be specified similarly.
Output:
[main] INFO spoon.Launcher - Running in NOCLASSPATH mode (doc: http://spoon.gforge.inria.fr/launcher.html).
[main] INFO spoon.Launcher - Running in NOCLASSPATH mode (doc: http://spoon.gforge.inria.fr/launcher.html).
test Comparator
[main] INFO spoon.Launcher - Running in NOCLASSPATH mode (doc: http://spoon.gforge.inria.fr/launcher.html).
test Comparator
So testComparator in Main was executed twice corresponding to foo1 and foo2 in App.