Joe, it's been a while since I replaced my passenger door window and I recall removing and re-using the proper screws and barrel nuts. I'm not sure there's room for a nut? The barrel nut seems like the way to go and at $6.00 for a set..........You might check a hardware store for replacement screws and barrel nuts. The barrel nuts and screws really maintain the integrity of the window frame when properly secured.
If you can use a small screw and nut that doesn't interfere with the window glass, it may be worth a try.
You might use the search function for using silicone instead of glass setting tape. I'm sure others will chime in and get you the info you need. Check this thread out:
(CLICK)Good luck,