During the “Us and Them” Tour, Roger has been playing what appears to be a vintage Fender Stratocaster on a few tracks. There isn’t much information online, but it’s clearly a well-worn instrument, which if it’s a genuine Fender, suggests either a custom shop model or a real vintage instrument. There doesn’t seem to be a CS logo in pictures, so my bet would be on the latter.
The small headstock and Transition logo suggest a 60’s instrument, earlier than the large headstock came in (very late ’65). To my knowledge, Fender don’t produce anything like this guitar at the moment.