It's certainly a plot hole that the people of the Source are not meaningfully different from the people on the First. Especially since the 7th Umbral Calamity tangibly changed people: before the Calamity, only those with the Echo could communicate with the various tribes, but after the Calamity everyone suddenly could. If I recall correctly, it's the same with being able to see Moogles.

That said, as far as plot holes go, it's thankfully not particularly impactful.