The Fuji X-A1 does not have an X-Trans sensor like the X-T1, X-E1 and X-E2 so I don't know how relevant this is to this discussion.They don't. It's a myth that a Fuji has lower noise than a Nikon (or Canon for that matter). How do I know this? I have a Fuji X-A1 and even though it does maintain color integrity up to ISO 6400 (which is a good thing but no better than my Nikon DSLRs) it doesn't have less noise.Why do the the Fuji X Series APS-c sensors seem to produce much better image quality than their Nikon and Canon counterparts....almost noiseless all the way to iso 3200. Granted, image quality may not be the only reason to buy a camera, but after reviewing countless images of all three with APS-c sensors, Fuji seems to have an edge.
I was under the same assumption as you before I bought one but I know different now.
Regards
Paul