I used to have a full-size spare. Back when I was autocrossing, I'd usually leave a tire in the well. Since I was carrying 4 race tires, there was no real need for a spare. Being the lazy-ass that I am, I'd leave one race tire in there all the time, rather than unload all 4 tires and put the donut back in
As for the lump, it wasn't all that bad. It was actually pretty handy for putting smaller objects tucked into the lowered corners of the trunk!
Styrofoam underneath sounds like a good idea.