If there is proper adhesive to glue tempered glass into metal automobile frames (they often don't use rubber gaskets these days) why wouldn't the same be applicable to a fiberglass structure which expands less than metal?
+1
After all, the principal component of gfrp is, um, glass.
Windscreen glue is amazing stuff; it's so strong it actually allows designers to use the rigidity of the windscreen to stiffen up the superstructure (insider info here).
Now for the bad bits: if you machine or rout a recess the thickness of your pane of glass, you'll probably go through the skin and be in the foam. So you could recess further and lay some mat & resin to give an airtight receiver.
Also most foams don't like uv so better to line your opening with gfrp and gelcoat.
Like your idea of doing double glazing, but there I can see potential issues (all fixable):
If you make a system that breaths then you risk letting humidity into the gap. That will leave traces you can't reach to clean.
If you seal it, you could put in a couple of those aluminium rails that glass cutter professionals use to assemble double glazing. They contain silica dessicant, which would solve your humidity issue, but then there's the altitude issue!
The pressure differences you could encounter MIGHT be enough to fragilise your assembly.
KTC Windows do it with sealed double glazing, but at 1000euros a window better to sort something out yourself.
They use laminated glass and security film, I would suggest using the same.
Or, to go back to the system with a breather, you could channel the breather through a little dessicator filter.
IMHO the completely flush mounted glass will look very elegant; it's quite fashionable these days, the big MPVs use that style.
BUT are you sure you want a window that you can't open? One thing you need in a small camper is ventilation, and windows are a good way to air the interior.
If you're talking about windows in the exterior part of the lifting roof, then they only have to be flush on the inside. With the previously mentioned recess you could mount a seitz (or copy) window without the interior cassettes. That would have no protrusions towards the interior. Ok it's not going to look nearly as cool as a flush exterior, but it would open.
These are just my analyses of the potential issues you might be faced with; please don't get angry with me, I didn't knock the idea, I actually quite like it.