I'm not familiar with the system, so not sure if this applies, but my doubles setup also comes with wingnuts and I had the same concern. So I replaced them with these, which are smooth and easier to manipulate.
DGX 5/16-18 Delrin Thumbwheel Nuts, Set of Two
Designed to be used in place of metal wing nuts when mounting backplates on doubles, the larger diameter of these Thumbwheel Nuts makes for easier handling so assembly and disassembly is a breeze.www.divegearexpress.com
I use the same nuts on my doubles. But, they don't make any difference to the OP's original question. Wing nuts are not going to stick up too far. The potential problem is the bolts themselves. If the bolts are too long, they'll touch your suit whether you use wing nuts or the Delrin nuts.
Different BPs have different bends. With the bolts for an STA it should never matter. But, with doubles, a plate with a bigger angle on the bends will sit further down (i.e. lower) in the gap between the two tanks. If the bolts are setup for a shallow angle BP, then they will stick out too far through the bolt holes in the BP.
Conversely, if the bolts on the doubles bands are set for a BP with a big angle on its bends, and then you try to use a shallow angle BP, the bolts won't stick through the bolt holes in the BP far enough to even get the wing nuts on them.
The DGX BP is really nice. It is a shallow angle BP. Pretty close to flat, as BPs go.
In contrast, the Blue Reef BP has much more angle on its bends. It's much further from flat than the DGX BP. Doubles bolts extend much further through its bolt holes.
I have both. Like I said, the DGX BP is really nice.
