The dimensions of the glass, and the metal frame, are the same for vinyl vs hardtop as the pieces are the same.
Your only difference is that the width dimension of the rubber as far as how far away from the glass it extends is very VERY slightly different. As in, IIRC, 1/16" or so different. Not much at all.
In fact, for cars that had the dealer-installed vinyl top the dealer would just use the original hardtop glass without switching the rubber seals over.
The goal/purpose between the two was for the vinyl top glass to sit more flush on the landau cars for a more finished appearance and to reduce water intrusion chances on the raised tip of rubber, wind noise, etc etc.
Any lexan you tried to use would have the same issue as the vinyl top gaskets - a small bit of hairline space between the edge of the lexan and the flush outer surface of the quarter.
If you try to insert the existing window back onto the fabric-less top you should see how big the gap is.
There ARE guys who use a solid seam of butyl tape and just run the quarter glass. If it's to be a mainly garage kept car that would cut down on the risk of leaking concerns over time as well.
The correct way would be to get the larger rubber seals, but, anything you'd do for sealing up the lexan you can probably do with what you've already got.