I highly doubt it would cause any flex or cracking problem. Many racers run fiberglass hatches. That's like saying your fiberglass hood is killing chassis stiffness. IT's connected the same way your hatch is. Two hard mounts, and one latch.
I also have a little rust
(
) on my hatch on the underside, and also looking to get a fiberglass one to keep the rust from ever happening again. I'd like to know from those with EXPERIANCE and not here say or rumor.