I'm attaching a hatch, so I imagine the screws are supplementary to the 4000 I'll use to bed it. I can't through-bolt, the overhead liner is in the way.
I would stongly suggest butyl rubber. I say this because I replaced a hatch bedded with butly a few weeks ago (broken lense) and it was a 10 minute job. Zero water leakage after 13 years. Easy to pry up, using a kitchen knife and a drywall knife. Easy to prep, easy to re-bed.
No, I don't use butyl for everything, like some fanatic. I use 4200 and 5200 other places. But on large items that are going to have to come off again some day (hatches, winches, cam-cleats, staunchians) it's geat stuff and easy to work with.
FWIW, the hatch was mounted with wood screws. Seemed like enough to me, but it was a deck hatch. I figure the screws were, collectivly, stronger than the latch, so through bolts would add nothing meaningfull.