VI,
Super Slow, the plan is to put a layer of fiberglass on top as well as bottom, similar to how it is from the factory. The gaps will need to be filled with something (other than fiberglass and resin). Would you recommend Bondo? VI could lay some fiberglass on the underside, then fill the gaps with bondo, and lastly fiberglass the topside. Also, how wide should the fiberglass strips be to get good adhesion with the top and how many layers do you think he will need both top and bottom considering the top will be inherently weak where the seams are. Would it be wise to start with a narrow strip and then go progressively wider as the layers build? Cosmetically the underside does not need to be anything special, and on the topside it will receive bondo and paint to smooth out any imperfections.
I
wouldn't use bondo as a structural filler. Its not designed for strength. I would cut some glass cloth into narrow stips. Mix up some resin and brush it into the gap from the under side, then pack the the gap with the cloth. Use a plastic paddle to push it in and smooth it across the surface making sure to get it as level as possible. Premember you have something (be it duct tape or something suitable like wax papaer) on the under side,(whitch will be the outer roof of the top) to keep the resin and glass strips from poking through the top and give it shape.
Then once it cures, sand it down some, and then I would overlay at least a six or eight inch strip (3 or 4 inches on either side of the gap) across the underside as a reinforcement patch. Don't forget to sand (rough up sand) the underside of the roof 3 or 4 inches to either side of the gaps for the overlayment to grab onto the old fiberglass.
Two or three layers of light cloth this way should give you enough strength you will only need one layer on the top. That will make feathering in the top patch much easier and less work.
Then use the Bondo to fill in the air bubbles and low spots in the top side finish. Use as little bondo as you can get away with.
Think of Bondo as nothing more than a plaster with the strength of sheekrock and your project will turn out great.
Bondo is an external filler for low spots in the finish.
Not a bonding agent.
I must confess though that its been a few years since I built anything out of fiberglass and there may be more products in the Bondo Product Line that I dont know about.
I found this out one time last year when giving advice about POR 15. I was giving advice based on the POR 15 product I'd last used 6 years prior and it seems they had expanded their line to do other things I wasnt aware of. I think it was a bed liner product they'd come out with, and this guy was talking about using POR15 as a bed liner and I thought that was stupid. Come to find out POR 15 Corporation had come out with a Bed Liner.

My Bad.
So remember the advice I'm spewing out is based on 10 year old technology. Old School knowledge. All these new fangled products dont always come through my shop. But, I do know some Pro's still in the field, if I need to update my knowledge base.
Have fun with it and do small area test to see if you like your method. If it works then do the rest of it that way. If not then you have only screwed up a small part and it won't take so long to fix.
SSR