Welcome!
Since your Boxster is a '99, you have a three-bow top so, if you want to temporarily install a glass panel in a cutout that you would make in the plastic window, you have to make sure that the glass panel is positioned so that it meets two criteria: 1. that it is small enough not to get crushed or cracked by the frame assembly when the top is completely open and under the clamshell, and 2. that its vertical size is small enough to allow it to end up stowed vertically against the roll bar so that you can put the top in the service position (to access the engine compartment).
Since GAHH makes a glass-windowed version of the three-bow top, the best approach would be to measure the size and position of one of those tops.
It may not be the most aesthetically pleasing install, but it should work if you can get some good adhesive for a plastic to glass seal. Note that your glass window will be considerably smaller than the current vinyl window and that your access to the engine compartment MAY be somewhat compromised, although that part remains to be seen (because the rest of the vinyl window will still be intact and that part will still be flexible).
Regards, Maurice.