Have to admit, I hadn't read that bit of the manual. I don't know what the active bonnet is :eusa-think:
I assume as long as the bonnet is securely fastened, the extra gap shouldn't really matter, although I don't think I would be happy going much over 30-40 mph really until it was looked at.
No idea how much that might be, depends if it involves any re-setting of this active bonnet thingy. A good body shop can often bend things back to where they are supposed to be, whereas if you go through insurance, they almost always just replace the lot, regardless of the extent of the damage.
Keep us informed of how you go on, especially with the active bonnet jobby.
Any photos of how it looks at the moment?