I had my MAF replaced...thankfully at the time I had the MS CAI so it was replaced no questions asked. But, I asked the service guy what would happen if I had had another intake...not Mazdaspeed brand. He said they wouldn't be able to work on it and I'd have to come back with a stock airbox or mazdaspeed part.
I really doubt the aftermarket intake 'caused' it to go bad, its them just trying to cheat you out it. They have to prove that the aftermarket intake was directly responsible for causing the problem. Easiest way is just bring it in with the stock airbox