If you're just filling gaps in a hole that's not perfect and will be under pressure fron the edge of the woofer, I would use polyester resin. This is the same stuff used with fiberglass and will soak into the MDF, particle board and will grab onto wood or plywood better than Bondo, although Bondo grabs pretty well. Thin is best but if the filler in the gaps won't be subjected to any major stresses other than vibration, it should be fine.
You need to wear a good respirator when you sand either of these, or when sanding MDF, plywood or any other wood products.