For my "no flange" top salvage at the Pick-and-Pull, I started with pulling trim covering the screws and removing the screws with my cordless drill (so glad I remembered to bring it). I was fortunate the screws were stainless, so I found a bag and saved every one, with the trim and the metal trim support.
Next, I went inside to look for a weak spot in the silicone sealant along the sides of the top, where the most light was coming through. I used this exact retractible style utility knife
being careful not to torque the blade for fear of snapping it at the "snap-off" lines and only exposing as much blade as I needed as I worked deeper into about 4-6" wide area of the sealant.
As soon as I got a purchase I started dropping in wood shims and a wedge to give the sealant a stretch and started cutting through the sealant with a slow back and forth with the utility blade stretched out. As I progressed, I advanced the wedge and shims, being careful to not stress the top too much. As soon as I got closer to the windshield I had to work from the outside. I did have a bit of satisfaction from standing on the hood as I worked my way around the front. I love salvage yards!
I finished cutting the top away from the outside especially when I started running into the metal top cage. Working by myself, this took a few hours IIRC. I did snap my blade, and took a lunch brake to visit the local Home Depot for a replacement. Since then I found these:
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1
They dont have the snap lines so less likely to break, and went with smaller 18mm wide blade so it has a little more flex to follow body contours than my original 25mm knife. Maybe worthwhile to find a handle that will lock too. I seem to recall while working the blade, it would retract unexpectedly.
For the flanged top, I would probably use a similar strategy, but probably start with deforming a convenient corner of the van roof enough to get a cable saw through. Obviously the cable saw will not work on butyl. Just my .02, no experience on this one.
Hope this helps.