Just that?
Yeah, it was Metal Sonic piloting, but Metal was doing a very good job pretending being Eggman in that game.
That just sounds like a nitpick then a big continuity mistake.

It's not like the plot is ruined by that minor "mistake" in a recap.

Dude, it was already stated that the comics don't follow the game's continuity as none of the previous games in particular have really happened as they did before aside from, apparently, Forces.

Yes, it's different. So was the Archie series. Different isn't automatically bad and thinking it is just makes you close-minded. Besides, who really even cares? It's not that important anyways.