Not a weird behaviour; PKHeX hides any species that are unavailable in your current save file (yes, this includes blank save files).
Ivysaur, Squirtle, Caterpie, Pidgeotto, Nidoran♀, Nidoran♂, and Abra are not available in SV, so displaying them in the pkmdb would be pointless because viewing the resulting pkm and trying to convert it to a PK9 would always yield an illegal result.
The setting you noted is simply there to help display everything regardless of availability, which is what you want.