Does the penetration need to seal?
Yes. And be removable. Here is the direction I'm leaning:
The deck fill will sit on top the finish floor, going down all the way thru the van metal floor. The rubber boot will go up thru the metal floor and seal around the deck fill pipe. Rubber boot will screw into metal floor from the bottom.
I may consider replacing the boot (or in addition to the boot) with a flat piece of butyl rubber and square metal frame screwed up to the bottom of the metal floor.
This setup let's me disconnect the plumbing drain pipe from the deck fill from under the van. Then lift out the finished floor (or the deck fill) from inside. It also allows for some slight movement between the finished floor and the van metal floor and drain lines.
The deck fill needs to sit flush with the finished floor as it will be the drain for my removable shower pan.
Also note that using the boot allows the seal to go up into the floor, leaving more room for attaching a right angle drain fitting as close to the van floor as possible, maximizing the angle drop into the gray tank.