My suggestion is to avoid screwing things to the inside shell of the hull, I feel an structural adhesive is the best approach. But it's not so simple as potting a plastic or metal battery tray directly to the fiberglass with some 5200 or Silkaseal, this approach is bound to yield the result you encountered.
Normally in a case like this I prefer to use a boat-building and repair epoxy to mount a piece of wood properly sealed and laminated with woven fiberglass cloth, then use the screw fasteners to attache the battery tray directly to the block of wood.
I use acetone to clean and remove the grease and oil from the hull, perhaps with a bit of sanding if necessary as well.
I take my kiln-dried block of wood cut to dimensions and coat it with a layer of activated epoxy resin then wrap that before curing in fiberglass woven cloth, like a nice Christmas gift, then coat the package with more epoxy resin. A paintbrush works great, and a plastic spatula such as an old credit or gift card can help, set that aside to cure.
This epoxy resin is about the consistency of 30wt motor oil until it begins to cure, which takes a few hours to complete after 12 hours. Pretty easy to work, with this pot life.
Then once the location is cleaned of lose paint, adhesives, etc. and degreased, I fully mix another batch of epoxy with activator and begin adding fine sawdust thickener to reach a thick peanut butter consistency paste for potting my laminated wood plank to the inside hull surface. If done correctly, this will produce a permanent bond of the wood piece to inside the hull and the wood will be completely sealed from moisture penetration due to the glass cloth lamination with epoxy resin.
You should have some duct tape available to use to make a dam to keep the resin putty in place until curing begins if necessary, or hold pieces in place, depending on circumstances. You may also choose to add glass cloth with additional epoxy resin over the wooden block if your prefer but this usually is unnecessary, depending on the desired level of finish.
Wait for all of that to cure, and you've got a nice solid surface well bonded to the hull for permanently mounting your hardware. You can mix a color tint into the epoxy resin if you like, or simply apply an epoxy single-part paint to blend the color into the area, these are quite durable.
It takes a bit of time but to me this is the best method, duplicating the standard method of boat construction.
