Not sure if it's because of a conflict with my other mods, but none of the "omnilation" recipes that show up in Factoriopedia (that convert various items/fluids into omnic water) show up in the Omniphlog's recipe chooser list for me. Are those recipes just some under the hood thing and not actual recipes or is something broken?

You might refer to the variations of the same recipe with different ratios? That would then be part of the original omnimatter code, which automatically upgrades recipes to a better version once you researched the specific improvement. So while there might be multiple versions, in game you would only see and use the best one you unlocked so far.

No, I mean the recipes under "Omni" in Factoriopedia, like "Lava Omnilation" that supposedly converts lava to Omnic Water in an Omniphlog. But those recipes don't appear in the omniphlog's recipe chooser.