I have a glass CJ where the PO had cut and installed a tailgate. He didn't do a good job. I closed the hole back up and made it solid again. Then I repaired all the cracks after all the flexing the body had done. You're going to have that somewhat anyway, but I think it is worse with that big gaping hole back there. That being said, do what you want. Make it look the way you want it to look.
When the term frame was mentioned, many tubs have 1/4 plywood sandwiched between the inner and outer layers to give it more stiffness or for mounting points. The plywood is found in stress areas. If you cut a hole, be sure and seal it up good so it doesn't get wet. It will rot between the glass layers.
A cutoff wheel is the best thing to cut glass accurately. It will not burn the glass. It will make dust! Cover yourself up as much as you can bear, then liberally dust yourself with baby powder anywhere you have exposed skin. The baby powder will help keep the dust out of your pores.
Last thought... if you use a tire carrier nobody will ever see your tailgate!
Go Fish! <*////><
But the right word at the right time... "Hey, give me a little hug!" That's the difference between lightning and a harmless lightning bug!