I mathed that out 2 days ago just theoretically and arrived at a similar conclusion. However, i'm still running 12-3 because it gives me at least one ampy per day and running 2-1 over and over gets incredibly tedious compared to just doing a few 12-3 + bonus stages and then be done for a fair while.

Also, coins spent will be a lot more with 2-1 because you only get lvl 5 and 20 manyus which will ultimately cost you a ton later on. All in all, 12-3 is just that much easier for those with a lot of high level characters in my opinion. Sure, if you can manage the gold for it, together with evolutions and stuff, by all means continue with 2-1.

I still agree that 2-1 is a LOT better for lower levels though, no doubts about that. But once your characters are in their evolved 40's you might want to look into 12-3 instead and get some ampys while at it.