It's been a while since I've worked with a BB, but I believe the non-drive side adapter is supposed to clamp down on the BB anyway, and not bottom out on the shell. If your non-drive-side flange was bottoming out on the shell, it wouldn't do anything to clamp up the BB. So, you should have a gap between the threads and the flange...it's correct. Shimano says to always torque the main-body side first, then the non-drive side. Specified torque is 50-70 nm (435-608 in-lbs) with grease.
If I'm off-base here, somebody please step in...as I said, it's been a few years since I've had the BB out.