My dad's TCs were always configured the way the OP is talking about, sliding rear window on the truck and removable window on the TC with a boot between. I always thought this was normal :) I also remember once the boot sprung a leak and we ended up with a wind storm in the back :E I also remember occasionally we would crawl back to ride in the overcab or play at the table, while in motion! Truck was Dodge club cab with jump seats, sometimes we needed to stretch!
My own Ford Ranger had a sliding rear window and snugtop shell with carpet kit I camped out of for several years. The sngtop did not have a front window, and I would leave the sliding window unlatched and store stuff in the front. I shimmied through it once just to see if I could.
I will just add something that is probably obvious. An aftermarket rear sliding window can be bought and installed by a glass company for any truck for a few hundred bucks, I would not let it be a deal breaker on any good truck. Also, TCs with a basement may be less likely to have a pass through window.
