My suggestion: Not worth it.
Several points:
1) My GTRV (Garageable-Top RV) based pop-top is about 3" tall, a "hollow" fiberglass shell. I wish it were taller. I have trouble getting enough room to tuck in all the tent material, and there's absolutely ZERO way I could leave bedding or extra mattress foam up there, which is a hassle. I have an ExPed 3" mat that I have to inflate/deflate every time I raise/lower the top. Adds 10+ minutes to what should be a fast activity. If your top was 3" of solid insulation, you'll have no place for ANY tent material, except hanging down into the van.
2) Sprinters already come with high-roof available - in fact, I'm willing to bet you'll find more choices with a high-roof than a low-roof (which means you'll have better price choices versus trying to find a rarer van). How many people are you sleeping? If its 1 or 2, don't even THINK of a pop-top, there's plenty of room for either permanent or temporary bed in a sprinter. If it's 3-4, even THEN I'd probably look at bunking or multi-layer bedding before I thought about pop-tops. Plus with a high-roof van you have room to move around without stooping over in the times when you aren't actually camping.
3) If you're thinking about insulation, you're really better off with a hard-roof and just lining everything with rigid foam. Take a look at the (many) excellent Sprinter conversions that have been done. No matter what tent material you use, and how many layers, a pop-top is still basically a tent. The R-value of the roof (and van walls) is totally blown away by the amount of heat you'll lose through the soft walls.