They should stick out slightly. I think mine stick out (at a very rough guess) about 8mm or so.
Also, there are 2 rubber bump-stops higher up on the side of the tailgate.
I find that by boot needs quite a slam to get it to fully shut, otherwise it half catches and rattles, and the alarm won't arm, etc.
Anyway, you can adjust the bump-stops with an allen key by inserting it into the centre of the rubber stopper. When loosened enough, you can push/pull the stopper to the position by clicking it in/out along it's ridged sides, then tighten the allen bolt again to lock in place. Might be worth minor adjustments to these if the lower plastic stoppers don't solve the problem.