My best guess is that it will work. I think back to DSi exclusives. Those didn't work because when you run the flashcarts, you run them as DS-mode software. Thus, any software run from them are also run as DS-mode. Gateway runs as firmware and Sky just emulates the whole cart. Thus, whenever software is run it should have N3DS specific features. A good example is Amiibo support with Sm4sh (actually I haven't tested this yet). In theory it should work barring any additional AP specific to N3DS-exclusive carts.
I guess we'll find out next week and see