I throw away nothing - I still have a box full of small foam chunks. The bits you carve out for below track level scenery, you glue back on to form the bits that go above track level.
As for spike holding - I last used spikes on a layout more than 20 years ago (ok, there was a long time in there I had NO layout...). The last two used adhesive caulk, and the next one will too. The ability of the base material to hold spikes is a non issue. In fact, the ability of the foam to take a push pin to hold track in place while the caulk set up was actually a benefit. They push in easily and they do hold with plenty of force to keep the track in place. If I used plywood, I would have to use the soup can express to hold the track in place. Push pins are quicker and I don't have to raid the pantry to weight things down.
I may use less foam base this time, but not through any dissatisfaction with how it worked on the last two layouts. I will be using a lot for the scenery, cutting and stacking it and then carving.
--Randy