For obvious reasons, having support for both firmwares in the same source tree is fantastic. Thanks a1ex! I've just tried building this branch for 1.2.3 and it builds fine and (superficially at least) runs on my camera.
I agree that 1.1.3 needs to continue to be supported, also agree that 1.2.3 can be discarded in favour of 1.3.3 in due course.
[Note that I'm not on 1.2.3 for external monitor support and I only use f/8 TCs rarely; the primary reason I moved to 1.2.3 is because I had been bitten by the 1.1.3 AFMA bug a few times]
It causes your AFMA values to get lost occasionally. The really annoying thing is there's no obvious way to notice it has happened, other than regularly check the Canon menus (or of course if you realise that all your recent photos are somewhat front or back focused!). I don't know if I was affected worse than most people or I have particular lens/settings combinations that trigger it on my camera but the bug was causing me enough frustration that I don't want to use 1.1.3 ever again.
I got this bug a few times as well, though I think I got it only after trying 1.2.1 and 1.2.3 and going back to 1.1.3 before 1.2.3 port was available. Either the AFMA value got reset to zero or set to some arbitrary value. I don't use f/8 that much either (yet, waiting for 100-400 II), but this makes me want to stay away from 1.1.3.