Looks like they're saved directly to the registry....No... I was wondering where the new save file location is, and someone told me to check AppData, but I already looked there and only found files from the previous version v0.2. Creating a new save in v0.3 doesn't change any of the files here.
So no, that's not where you put the save files. I gave up looking and still don't know either.
HKEY_CURRENT_USER\Software\Team Bieno\Breeding Farm