Fiberglass, safety glass, plexiglass and polycarbonate (lexan) all have different coefficients of expansion. Thus the window has to be "floated" on the sealant. For glass M Windo-Weld 08609 is often used on cars, and should work well with fiberglass.
I replaced the main cabin (Pilot house) on my Cal 46 and used a GE specific silicone for the polycarbonate (which had a non scratch coating), We set the lexan about 1/8" off the fiberglass with cork/ruber gasket material, to allow the expansion. We overlapped the fiber glass by about 2" all of the way around. The windows were a fairly dark color--and the black sealant didn't show at all. We accidentally got a "gob" of the sealant on the SS rigging. It was still there 8 years later when we sold the boat--despite over 40,000 miles of travel, and the sheets
I would do the same thing with glass: use the M Windo-Weld 08609 , use some cork gasket material to space the window slightly off the fiberglass. The glass will have to be held in place with tape until it sets up....not always easy to do.l...
The "H" rubber gasket is probably easier than a sealant/adhesive. We over drilled the holes in the lexan, and put plastic washers to avoid stressing the lexan. You could have a few holes drilled to hold the glass in place while the bond sets.