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That would be terrible, imagine what it would do to the value of the car. Don't band-aid it, pay up to replace the weatherstrip or whatever is out of whack that's actually causing it to rattle.
The top attaches to the car using the large steel brackets at the B-pillars and at the windshield header. The encapsulated bolts at the decklid do not have anything to do with structal rigidity.
If you tried to permanently glue the top to the decklid, the chances are that the decklid would crack or tear away from the hinges.
If the top is attached properly by following the instruction sheet that came with the factory top, there should be no rattling.
By any chance, did you accidnetly hit one of the decklid release buttons with the hardtop installed? When that happens, you usually get rattles and then you have to remove the hardtop, then raise and close the decklid so that the locks engage the decklid pins.
The top attaches to the car using the large steel brackets at the B-pillars and at the windshield header. The encapsulated bolts at the decklid do not have anything to do with structal rigidity.
Those rear bolts only seem to draw the rear deck lid up to the weather stripping for a good seal.