Title. I think this is because RS replaces vanilla's stronghold with its own. Perhaps add support so compass can track down their stronghold?

This is because Repurposed Structures removes the vanilla strongholds with it's own. You can turn this off in Repurposed Structures's config. Furthermore, you can set the config in such a way that modded biomes have Vanilla Strongholds and vanilla biomes have RS's Stronghold. However, Eyes of Enders will always point to the closest Stronghold as I made that item check all 3 strongholds (vanilla's, RS's stonebrick, RS's nether strongholds) for the closest. You can also do /locate repurposed_structures:stronghold_stonebricks to find it as well.

You have a few option here of what to do. Nature's compass can add support for my stronghold but that's up to them.