I like your Arno / Controller long con theory. Slott made Arno so sinister a couple of issues ago (allowing a herd of cattle to trample over Wayne, etc), I think a scheme to claim Howard and Maria as his parents might be something that Arno would do. And, that's a scary thought that Tony's hard drive was in the Controller's possession for who knows how long.
One more thing I noticed: When Amanda picks up the family photo in this issue, it's a photo of Tony, Howard, and Maria. It then changes into Arno, Howard, and Maria...BUT, when Howard arrives on the scene, Tony reappears in the family photo. Also, notice that Tony's "home setting", the restricted settings that he programed himself, features Howard and Maria...and not Amanda. Yeah, Tony is aware of the deception, and he's making a big dramatic point here (maybe).
Of coarse, Tony keeps calling Amanda "Mom", but that could just be him "playing along" until he decides to end their con.
At this point, I would even settle for Amanda being a skrull.