Not sure how much plumbing work you guys have done, but the Toilet goes right into a 4 " main with no TRAP, like under a sink or even like the shower
There is a wax seal there for a reason. There may be what we call a Lead Bend there ,but its not for trapping gases as its horizontal .
The "trap" on a toilet (to hold the gases from leaking) is inside the design on the toilet itself.. if you ever break one apart you will see it..
So If you gonna raise the toilet, better make it cement and tiles, with proper pipe and connections to that 4" main and a wax seal at the bottom of the toilet, dont go messing with a plywood box cuz it sounds like a recipe for disaster.