Typically you will be installing some type of sub floor (van). Cargo vans have uneven floors. A series of peaks and valley’s in its metal sheeting.
Finished Passenger vans often have a more finished level floor. But they may come with bench seats you now have seat lock down tracks to contend with.
I have a passenger van. I am pulling most of the bench seats. In my build (with the thought of being able to return it to its factory state if need be), I am covering the existing factory finished floor. Covering everything such as seat lock down tracks, and D Ring tie down points.
I am using 3/4 inch plywood with strategically placing 1/4 plywood on the underside facing the van floor. To shim it higher than any protrusions. This is to miss the track and D Ring hardware that is slightly higher than the factory floor.
This new base covering will flatten everything out. I used existing track bolt locations since there were factory welded nuts that made ideal anchor points. It required removing the existing bolts and replacing them with longer bolts.
Don’t cut the sub floor plywood too tight on the edges or you will create squeak points when driving down the road. It is better to have a 1/4 to 1/2 inch edge gap. If you want to fill the void, use some type of caulk that remains flexible.
You can counter sink your anchor bolt heads or use “Cup Washers” to get a relatively flush mount. I intend to have a finished covering of spun rubber commercial interlocking carpet squares. over this plywood sub floor. That type of carpet can be installed over “Cup Washer” installation and never be noticed. If need be, the bottom side of the carpet could be routered out a bit, just above any “Cup Washer” location.
Another method, which we are incorporating is to use the existing seat track, and fabricate adapters to create floor and wall partition anchor points.
If you intend to install some type of vinyl finished flooring, you may want to counter sink any bolt heads. Or use Elevator bolts through new holes drilled in the van floor, with washers and nuts under the external floor of the van.
Plan before you drill any new holes through the floor. You want to miss the frame and any other critical things like fuel lines, electrical, brake lines, etc.
For thin vinyl flooring you may want to fill any counter sunk bolt head voids, flush.
I personally don’t believe counter sinking would provide adequate anchor strength. It would be my third choice, after a Elevator bolt. Counter sinking, and even using a washer, would remove at least half the depth of the wood. You have to think of the weight of other items that will attach to the sub floor. Then the stress and strength to remain attached even in a moderate vehicle accident. If you are OK with that method, then it is an alternative.
Once your sub floor is installed and secured, you can proceed with your layout and build. This will provide an excellent foundation to draw your layout on, secure partitions, cabinets, or attach hold down brackets for things like water tanks and batteries.