Through bolting them with the proper bedding compound would make them far more secure than using just a sealant alone, even 5200 wouldn't be as secure as having them through-bolted with a proper backing plate.
If you're worried about someone unscrewing the bolts... put a second locking nut on the inside...and that should prevent them from being unscrewed without access to the interior of the boat.
I'm not worried someone would unscrew them, if someone wants to get into a boat, they will.
I wanted a cleaner look that offers more resistance to water intrusion, and no more varnish or teak oil. The trim peices that are there now let in a lot of water, so redoing the hatch boards w/ acrylic and changing the tracks from 2 peice to a one peice C section track would help that. The track is only wide enough to fit the new boards in, no room for the heads of screws. The aluminum is also thin, so countersinking wouldn't leave much material for strength.
I'll try to get some pics this weekend.