when I bought my 372. I asked what to do when my plexi needs replacing. They said either bring it back to them or send straight to PASC. So I asked, if I have to send it in to get it replaced, what's the point of including the spare? I'm paraphrasing the response just a bit, but by including the spare plexi, Panerai is basically saying to owners - "hey, this is a "wear" item - it will need to be replaced from time to time, and your first one is on us." They went on to tell me that the cost of plexis is negligible compared to a new sapphire crystal.
My point is that I encourage you to think of the plexi the way you would think of tires or brake pads - meant to be used, worn, replaced - without compromising the integrity or value of the piece/car.
On the other hand, replacing the plexi with sappire does compromise the originality of the piece. So even if you could do it (and apparently they won't), I wouldn't.
My advice: wear, enjoy, and when the plexi gets too marred for your tastes, pop in a new one!