Glueing the flaps is what holds the model together so I would figure it should work fine. I've never had any pull up on me. Or do you mean will the resin soak through? The glue provides a barrier but it is pretty thin and shouldn't affect the overall structure much.
I mean if there is a lot of glue on a flap(hot glue) and you go to fiberglass it, will that lump show up as a big bump in the fiberglass or will the resin create a thick layer that will cover all of the bumps of glue and raised flaps
If you use cloth then yes, it will mirror the surface you put it on (still if you're talking about 1/8 inch or less it shouldn't matter much). Matte, I think will reflect it less.
You could add some Krylon clear coat sealer. It should prevent seeping through. I plan on using it as soon as I can find a walmart that has some in stock. e