If you look at the back side of the zipper when it's fully open, there is a strap sewn across the back of the zipper at the end where the pull is when it's open. That strap keeps the zipper from being pulled so that it makes a sharp angle against the slider.
Thus why it's okay to have the zipper fully open.
Having the main zip open and the protective flap zipped shut seems to have no point. To me, the reason for leaving the main zip open is if you're hanging it up and want the suit to be as open as possible to dry out the inside. You don't want the protective flap zipped shut when you're doing that. And if that's not your purpose, you may as well zip the main zipper shut.
The main zipper is MOST protected when it's fully shut. Store it that way when you don't have a reason (like drying the inside) to have it open. When you do want it open, just make sure it's FULLY open.
Or I'm missing something?