The problem I have with this mod is that when you make the window opening smaller to make that small gap around the glass, you are changing the look of the back of the roof more by making the window "smaller" than you are by the "Trick" flush mount. That body has a little line around the rear window, the distance from the glass to that line is further when you do this, do you really want that?
The chrome around the glass makes for a "larger" window in your eyes. Even though it covers up a bit of the glass, bringing the body to the glass and eliminating that cover over it doesn't make the glass bigger, it makes it smaller because the chrome was effectively the "window".
What is your "theme" for the car? If it is modernizing it and shaving off all the chrome around the tail lights and flush mounting the bumpers, shaving the drip rails and so forth that flush mounted glass fits right in. But if all those things aren't being done, what will flush mounted glass get you in the overall look? Are you doing the windshield too?
I ask these things because if you were doing all those things you wouldn't need to ask the question on how do you flush mount the rear glass, you would be on top of that like butter on toast. So if you aren't making all those other mods, why do this window?
Basically, if you want to make the rear window flush mount, first decide on what moulding if any you are going to use. If it is the S-10 style little rib of plastic that is about 3/8" wide that moulding needs about a quarter inch gap (a little less as I remember) to slip into to. So you get your glass and using IT as your guide make the hole a quarter inch bigger than the window.