The AIU control isn't the issue, it's the track signal that's the issue. The AIU is connected directly to the TIU and to the switches & accessories, no track signal issues there.
IMO, that is a mistake, but the proof will be in the running of any MTH DCS locomotives.
I generally run my MTH locomotives in conventional mode. Occasionally, I will dial up track power with the remote on a command loop, but not too often. Given that I can not access any features with Legacy, I do not worry too much about it. If the common ground is only an issue with MTH engines, then I think I will be OK.