Nope, it’s all separated now.
Once you get to the new continent you can visit the trainer and learn Zandalari Enchanting whenever you want. Within every one of your professions (except Archeology) you’ll notice they now have separate skill bars per expansion.
So you could have Legion enchanting 20/100 while having Zandalari Enchanting 150/150. BfA recipes require Zandalari Enchanting skill, and Legion recipes require Legion Enchanting (so just as you would expect).