I run my settings very similar and as you said the Mark II lead is much rougher than the Mark III. The gain boost is over the top and very dark, I need to play with that more. I also find the clean channel on the IIA amazing. The head room is limitless and crisp, as good a clean Fender sound as I've ever heard. That said, I prefer my III Blue overall but since I have both I use the R1 of the IIA for cleans and the R2 and Lead of the III. The R2 on the my Blue in Class A is just awesome. A full chunky slightly broken up sonic wonderland. I've been able to dial up some of my favorite rock n roll sounds on that channel. Last night I was rockin to Ron Woods "I Can Feel The Fire" and it sounded just like the live version (because of the mistakes) in which he uses that exact amp. Mind you it was all at indoor levels another benefit of the Mark III they sound so good at low volume. The IIA is less well behaved at low levels, it hasn't learned to play low, it just likes to scream.
I'm thankful to own both, they are a blast to play.