Crusty Old Meatwad (he/him)
Yeah, the Elves of the High lineage and the Elves of the Wood lineage are the same species. They can obviously reproduce children with each other. The children can drive traits from both of their parentages.
There is only one species, the Elf. This species lacks wings and lacks waterbreathing.
So, when one happens across a community of Elves who actually have wings (Avariel) or who can breathe water (Sea), this particular community of Elves obviously acquired these by means of magic − because they arent species traits.
As a species trait, Elves do exhibit innate magic. And by means of this species magic, certain communities can acquire effects such as wings and waterbreathing.
I just don't see you getting wide buy-in for this idea. I don't think it's a crazy idea or anything, it's just too contrary to tradition to get sufficient support from the wider consumer community. I also don't think you've thought through some ramifications like anti-magic zones and the impact that has on what is considered innate abilities.