Very good idea and good job.

I just did something similar to mine last weekend. I simplified a little by using a 1/2 thick sheet of MDF and cut it out in the same shape as the styrofoam piece that sits on top of the spare. In that I cut the center hole for the exact same Pioneer 10" sub that you used. Once it sits into place (just like the styrofoam piece) I shimmed (sandwiched) some left over 1/2 inch MDF in between another piece of 1/4 inch MDF that I cut out to match the small corrigated piece of plastic that sits on top of the spare and under your carpet. What this did was make a solid deck that when I put the carpet back in, the speaker did not stick up above the floor level. I then put a level guard over the speaker to protect it and now I can put anything back there and don't have to worry about poking the speaker or anything.
The entire project took less than 2 hours and cost less than $20. System sounds great without a speaker showing anywhere.