The original lower crash bars that BMW included (the forward piece on the left of this photo) might give the impression that they'll protect the cylinder heads, and such may be true in the perfect crash scenario. Can you make sure that you only put your bike down at the perfect angle and speed to utilize the original crash bars? Didn't think so, and BMW knew this when they designed the original bars. They've given us the 'impression of protection,' and know that anyone who's boxer engine hits the ground will be buying parts and/or service from them shortly after.
Enough conspiracy theory rambling.
Instead of crushing the aluminum cover and either causing leaks in the valve cover gasket or causing much more extensive (expensive) damage to your engine or other parts, protect your bike from the start with these Engine Guard Extensions, made by Adventure Designs.
These engine guards cost less than what you're likely to spend the first time you put your bike down. (Just 1 original aluminum BMW cover alone costs about the same as both Engine Guards from Adventure Designs.) If you figure you're never going to put that nice new bike down anyway, sadly, it sounds like you won't be using your GS Adventure to its fullest potential!
(Below: A picture of the original bars BMW "pretends" are sufficient protection; Bottom: The Adventure Designs crash bars supporting the bike!)