If it contacts the wasteboard along a line, you could add double sided tape there, in addition to side clamps and wedges to support the parts that don’t touch the wasteboard.
I frequently use painters tape & bondo. I’ll place the board cup side down & grain going in the direction of cut & trace a line around the edge. Place squares of tape on the spoilboard & put a blob of bondo on each square. set the workpiece in place & apply a little pressure to squeeze the bondo, then let it harden.
Surface the first side, then when you flip it the bottom is flat & you can use tape & glue or 2-way tape & side clamps.
Interesting method - Do you squish the stock directly into the bondo? And if so, how easily does the bondo release from wood? Or are you putting painters tape on the stock as well, so the bondo is touching tape and not the stock?
As it is a full flattening pass, do it manually. Use virtually any long clamps to hold the edges down then move your cutting bit back and forth along a path until you reach the clamps. Then move your clamps to the flat part and pick up the process from there.
In so many words, don’t bother writing out the toolpath, just do it using the JOG feature.