I've been down this road a few times. I've never owned a pop-up, but it makes no difference regarding the concept. I also wanted the pass-through access for our dogs.
Initially, I used an inflatable boot that spanned the width of the cab. It worked well to seal the opening against the elements, but it required monitoring when we changed elevation to prevent over- or underinflation.
I tried a manufactured foam wedge, too. I don't recall many details but I'm not using it now so there must have been some deficiencies with it.
We currently have a Callen cab-over shell with standard sliding windows in the cab and shell. I made a gasket out of 1" pipe insulation by measuring around the pass-through opening and then mitering and glueing the corners. It's like a foam picture frame that gets wedged between the cab and camper from inside the pass-through. Because it's outside the perimeter of the windows, both windows can be closed and locked. I don't have any leaking while parked or traveling down the road, despite living Western Washington.
There are two types of pipe insulation; one is a harder, "plasticy" foam and one is a softer rubber-type. The harder foam is more durable but the movement between the cab and camper will make it squeak and drive you nuts. The softer foam seals better and is quieter.
I have the opening mostly for the dogs but I can get through it, if necessary.
