All the windows make it harder to insulate, need some kind of covering for privacy, make stealth camping more difficult, and make it easier to break into the van.
Glass has a lower thermal conductivity than steel. If equally insulated, glass should modulate temperature better than the steel that surrounds it.
Privacy is an issue that can be addressed on a temporary basis using removable insulated window covers or by permanently installing insulative material over the windows.
The side windows of vans is not the weakest link for break ins. It is much easier to jimmy a lock, or break the driver or passenger window to access the door lock.
I don't know what stealth means. Most folks don't pay us no mind unless we give them a reason to. Window vans are a lot less frightening than cargo vans. No one looks at a window van and wonders if anyone's inside it.
The seats need removed and disposed of, which is extra work, and leaves holes in the floor to be patched. Most passenger vans I’ve seen have coverings on the side, which they tell me aren’t well insulated, so would need removed and insulation installed, and I’m not sure, but I’m guessing would be more to dispose of with the seats.
If you're looking to get down to the bare metal walls, then passenger vans are certainly more work. I'm suggesting that in many cases that's unnecessary. I don't know about all vans, but the Transit and Sprinter have seats that are quickly and easily removable by the simple pull of a latch. Undesired seats can be sold for hundreds of dollars per row.
The OEM seat mounts in the floor are useful. They can be used as attachment points for furniture that will be installed in the buildout. If more flexibility is desired, they can be used to attach sheets of plywood, creating a new (and well insulated) floor. My van floor was a composite material covered with vinyl. I laid plywood overtop, covering all the seat mounts except a cutout preserving the ability to add/remove the second row of seats at will.
The uncovered walls of cargo vans require immediate attention since they are ugly and can get uncomfortably cold/hot to the touch. While there is no insulation in the walls of most passenger vans, the interior coverings are aesthetically tolerable and pleasing to the touch. Insulation is a good thing, but it is not a replacement for mechanical manipulation (ie. heater, fan, AC). With adequate mechanicals, I have not found myself wanting for insulation. If I ever need to get behind the OEM panels for some reason, I will probably stuff in Thinsulate before reinstalling the OEM panels. I could not make wall coverings that look as good as the factory panels.
Here's an example of a well done buildout using a passenger van:
Also, while I do see more passenger vans available, and some do have a little better pricing, high or even medium roof passenger vans are rare unless it’s a wheelchair van, which I have been warned away from.
The Sprinter and Transit are the only two OEM hightop passenger vans. So there are relatively few on the market. And the Transit has only been around for 7 years here in the US.
No question it's a hot market right now, there's also no doubt it won't last forever. So it really boils down to what matters more: your money or your time? Spend more money now or wait and hit the road later.