I think your concerns are pretty understandable from a field ecology perspective. The question which I don’t know how to answer, and haven’t seen answered satisfactorily anywhere, is how does iNat apply this conception practically at an international scale?
I find phylogenetic lab taxonomy frustrating sometimes because it can result in a lot of cryptic species as you mention (and has been discussed in other threads extensively), but creating a parallel phenetic/macro-morphology based taxonomy for all the plants in the world from scratch seems excessively daunting to me. But I kind of feel like that is ultimately the only option if we take this argument to its conclusion, and reject all the other world plant taxonomy authorities that are available.