Yes, vanilla breeding mods clash with this. Unfortunately there are only a few possible solutions.
-1. People who make breeding mods could make their animals be a copy instead of overwriting.
-2. People who make breeding mods could make rescaled versions of the now breedable animals.
-3. You could drag the breeding mod higher than this in the load order (the animals affected by the breeding mod won't be rescaled but the rest will)
maybe there are other possible solutions as well.

My only gripe is that it removes the Ocellaris Clown's ability to breed and create hybrids, but I think that's the two mods clashing.

Yep. Some of the species in the vanilla game were upscaled quite a bit in order to not be size 1. Mainly with Freshwater Frenzy, anyway, as a lot of the popular freshwater fish would normally be considered brokenly small.

This is one interesting mod so far. The guppies are now utterly tiny...which actually helps in my mega livebearer tanks, since it balances them out a bit.