I don't think that it should be a problem. It's actually much easier to handle than to play several Tournaments with different structure at the same time.
Do it all the time playing different stakes from freerolls for example as they are pure +EV simultaneously with $100+ buy ins tables as smaller percentage of rake taken by the house over a $100 entry compared to the smaller buy ins.I am staked for 02/05. Is it a bad idea to multi table and play say two of 05 and two of 02? Will this hurt my game? The way I see it the players here pretty much play the same.