I don't like the idea of Dremel-ing aluminum to make things fit, but I honestly don't see a stiffness/weakness issue with removing 2 of the 4 mounting holes. It is possible that the entire hole would have NOT to be hacked off, maybe just angled and use a much shorter screw to secure the top deck to the bulkhead.
And, yes, Dremel-ing a Lipo case probably isn't so smart. This 511 is getting me excited, ok?!

Dave, get that camera in your hand and take those pics!