The A-Wings in FC aren't, iirc, anything special that I remember? I haven't played in so long though, but still have the strategy guide here somewhere and the cut scenes saved somewhere for a customizing ref.
As the EU goes, the A-Wing was around LONG before ANH in some capacity already. It was the retconned into the ICS books as the Arrowhead Fighter (basically A-Wing ancestors that looked just like them), and that they were at Yavin... This jived with X-Wing (PC Game) and Rogue Squadron and such. The B-Wing wasn't really changed much either. It's still the project Shantipole thing more or less... They just wove it into Rebels, and added their own stuff that doesn't really change anything. Also it's still a prototype type deal, and seems on pace for its introduction as a production ship before the Battle of Hoth (roughly).
I should check that Force Commander guide out on the A-Wings... It's possible, as with all types of military weapon, it's just a weapons or shield or other enhancement too... It's always easy to crowbar that in without it really being contradictory.
The Y-Wings in the episode actually don't even appear to be the same ones from TCW but may actually be them fitting MORE EU into the new "canon" (or, new EU Disney's making), as those ships REALLY looked more like the up-armored Y-Wing from the Incredible Cross Sections which pre-dated the Clone Wars ships, and which helped cover up the fact the Clone Wars ships were too big to be the Rebel Fighters, actually, if you're going strictly on visual comparison. They sure appear to have the more tight-fitting armor plating though, like the ICS armored Y-Wing design had.
EDIT: Yeah this piqued my curiosity so I looked into it... Someone just promised a group of A-Wings if they helped him or something. It's a later mission (rebellion one) and those ones were so inanely frustrating I think I blocked them out, but yeah they actually show A-Wings in Rebel hangars when the main character defects long before that A-Wing mission and stuff.
Oddly, the old EU actually kept that stuff sort of straight.
A lot of other stuff they couldn't and Disney obviously can't keep it (or at least not all of it) and make $ on the investment and stuff, but it's funny when you look at some really small details of EU and they kept a lot of it in order... They seemed to almost goof up bigger stuff more often.