In sass custom-properties are unfortunately just treated as a string, it doesn't associat a value.
However there are workarounds:
@function get($var) {
  @return map-get($custom-properties, $var);
}
$custom-properties: ();
@each $key, $value in $custom-properties {
  :root {
    --#{$key}: #{$value};
  }
}
Add any variable, you want to use within your Sass project and also be compiled to a custom-property, to this map: $custom-properties: ();.
$custom-properties: (
  'navbar-transparent': true,
  //...
);
Now use get($var) to acces said variables within your Sass project.
@function get($var) {
  @return map-get($custom-properties, $var);
}
$custom-properties: (
  'navbar-transparent': true,
);
@each $key, $value in $custom-properties {
  :root {
    --#{$key}: #{$value};
  }
}
@if (get(navbar-transparent)) {
  .nav-booking {
    position: absolute;
    width: 100%;
    background: transparent;
    padding-top: 20px;
  }
} @else {
  .nav-booking{
    border-bottom: 2px solid #d6d1d180;
  }
}
This will compile to:
:root {
  --navbar-transparent: true;
}
.nav-booking {
  position: absolute;
  width: 100%;
  background: transparent;
  padding-top: 20px;
}
https://codepen.io/LudwigGeorgImmanuel/pen/dypaXyE