Welcome to the 'fine print' of the NEC
Using the 'wild leg' for the 240v circuits is never a code problem. If the panels have ONLY 240v circuits in them, you don't have any code problems. It's the presence of the the neutral, which suggests that there are 120v loads, that creates a code problem.
Look at the tiny print onside the door of the main panel, on one of those upside-down stickers. It will list the power distribution systems for which the panel is listed. Where it mentions 240/120 Delta, it will say something like 'multipole only.' In other words, you're not supposed to have 120v circuits originate from that panel.
Yes, I recognize that there are millions of panels out there where they simply skipped every third space. There are also a multitude of 'split buss' panels out there tht were developed to specifically adress this issue.
So- what are you supposed to do? As best as I can figure it, you are supposed to take the two "normal" legs, and use them to feed a separate panel, from which all of your 120v. loads will originate. Otherwise, you're using the main panel in a way not consistant with it's labelling - an Article 110 violation.
The second half of this answer is a bit more subtle. Can you see the transformers that supply the place? Are there two transformers (one larger, one smaller) on the pole? Or, are therer three, with one much larger than the others? The point I'm getting at is that you probably want to talk to the PoCo about getting "real" three phase power if you either have serious three-pahse loads, or a lot of 120v loads. You want to consider changing your place over to a 208/120v "Wye" system.
The change in voltage from 240v to 208v IS a problem if you are using it to create heat. It should not be an issue for motors and the like.