I noticed this while working on compatibility with my own mod. Here is a decompilation of the actual injection.

   public class_6861(class_3264 $$0, List<class_3262> $$1) {
      List<class_3262> var8 = this.localvar$zzi000$enhancedblockentities$enhanced_bes$injectRRP($$1);
      this.field_36390 = List.copyOf($$1);

The list you return from your ModifyVariable handler (var8) is never actually copied, so the resource pack is never actually added to the final list stored in the resource manager (only to the namespaced resource managers).

I was using 1.18.2 for testing but I think this would occur on any version with the mixin.