Your point about the rushing is why I'd start with Tommy and play the offense we're going to play. I don't think it has to be different with the "running" QB. Tommy actually looks as fast, if not faster. He's just not as accustomed to it, so it doesn't always look fluid. He still needs to take a hit better, know when to slide a bit quicker. Seems to be improving though.
In the past we avoided this because if Tommy got hurt, plan B was really plan Z. Now there's a plan B, maybe even a plan C, so let him run RPO, designed QB draws, take off if there's trouble and try to get to the edge. Who knows, maybe it even makes a team think twice about pinning their ears back and going after him.