Note: I have a LaRue MBT in mine, but I can see the same mark on the receiver in front of the hammer. On mine, if the upper receiver is not in place and the hammer is not in the cocked position, a lower part of the hammer rests on the receiver. When the upper is put back in place, the rear of the bolt pushes the hammer back a small amount and the hammer is no longer resting on the receiver, but on the rear of the bolt. Have your upper with the bolt carrier group in place and the hammer not cocked. Pivot the upper back into place and see if the hammer moves back. If the hammer moves back from the bolt, I do not see how it could be contacting the lower receiver during normal operation. I bet it only takes 1 or 2 times of inadvertently letting the hammer go forward under hammer spring pressure without a bolt installed to make that mark.
Regarding the gap behind the bbl locking lugs...mine looks just like yours, and I've fired 2054 rounds through mine.