Fabric Waystones says that it supports it, and I saw that you've mean a pull request not too long ago to add native compatibility to FWaystones, but I tested it out on a fresh instance and no waystones are spawning.

1.21.1 Fabric
RS: v7.5.13
FWaystones: v3.3.4

That is because the 1.21.1 jar of Fabric Waystones is still using the 1.20.1 rs compat files instead of the 1.21.1 compat file from this PR: LordDeatHunter/FabricWaystones#269

So no, this is not a bug in Repurposed Structures. This is Fabric Waystones using the wrong files. @LordDeatHunter can you please release a 1.21.1 jar build with the linked PR's file changes?

Will drop a new release once LordDeatHunter/FabricWaystones#277 is ready for 1.21.1 as well.