My experience with prefabbed boxes (ran one in my 14CC) was that the top section (that sat above the lip in the floor) was at minimum 3". I can measure the prefab box as i still have it in my basement when i get home. The fitment of the bottom wood section only fits into the floor recess very crudely... basically looks like a funky misshaped bucket and leaves LOTS of space unused. This is why the fiberglass bottom is the best option as it wont be thicker than 1/8" and it will use EVERY bit of space available. So your gaining the unused space the prefabbed boxes don't even utilize and your gaining the thickness of the MDF they use 1/2, 5/8, 3/4".
Also the bottom "floor" of the prefab boxes is what sits ontop of the storage space lip... so you would have to take the box and cut the bottom bucket area off and then trim it lower as your sub top surface has to be lower than the top of the lip otherwise the fold flat floor will contact it... also the sub cone will protrude above its resting surface as its used so you have to give yourself added space.
Your better off starting from scratch as literally you would be junking 80% of the preffabed box and you would be getting all the required sqft for the sub (limiting yourself immensely). Just do one solid layer of glass in the truck, mix it heavy on the hardener and in 30min pull it out, then add extra layers on the inside when its out of the truck. The issue isn't going to be the smell of the glass when its in the truck setting... it will be that the box is going to smell for a while afterwards... like a few months lol. So unless you plan to leave it out of the truck for 2 months after finishing till it stops stinking then your going to get the smell either way.
The good news is my setup doesn't smell anymore and the sub and box have been working great! Ive actually had to turn down the LOC signal as it was pushing too hard and rattling things in the truck.