My preferred answer to the original question is a very complex one that I don't fully understand myself, one based more on thematic reasons than literal ones. It essentially revolves around the concept of an individual (Robotnik in this case) being enslaved to industry, rather than the other way around. It's based off of some rather confusing philosophical writings I had to read last year. I think I've got a slightly better explanation written down somewhere. I'll try to post it later.
The easiest explanation for King Max being in Ironlock is that, by traveling back in time, Sonic and Sally create an altered timeline, in which the rest of the series takes place. "Sonic Boom" takes place in the original, unaltered timeline. It's entirely possible that Max originally was never cast into the Void, or that he was originally held in Ironlock for a time before being sent there.
That said, it is difficult to determine a specific action taken by our intrepid duo of time travelers that led to these changes. It could have been any number of minor things, with the Butterfly Effect working from there.
Rosie's fate is already indication that everything set after Blast to the Past is in a different timeline. It's not unreasonable to assume that there were other changes as well. And yes, before something brings it up, this means that Robotnik's arm would have originally been roboticized in some other way. Having Sonic be responsible is still significant, however, as it worsens Robotnik's obsession with the hated hedgehog to the point that it helps lead to his downfall.
I'm not sure how the cell being booby trapped is significant one way or another. That said, I'm fairly sure there's a required quota of booby traps in terrifying, ancient dungeons.
The robot-monster could have been a cast away experiment of Robotnik's, perhaps as part of a program to imitate organic life using machines, whether for espionage or to prove a philosophical point.
I can't think of any questions myself off the top of my head. I've rationalized most of the questions the series raised.