I'm currently using this mod to generate an assortment of different versions of chunks with the intention of loading them in a Vanilla server, however, a slew of warnings are thrown upon doing so.
I've got the biome generation set to 'vanilla' so the chunks themselves should be fine; however, I'm wondering if this mod using custom structure names (like for the ocean shrines) will adversely affect something somehow.

Yes, the modded structure references are likely the issue here. You can try using this tool to remove all references to modded structures in every chunk you're trying to import: https://github.com/Nyveon/MCStructureCleaner. Please be sure to back up your world before running this tool, as it appears 1.18 worlds may not be fully supported.

Ooooo thanks a bunch! This seems to be what I was looking for. I've been using 1.17.1 just in case anyways to avoid any potential compatibility issues with 1.18, so I should be good. Thanks again!