My question is am I making a mistake by doing the work with the boat on the trailer if so I what’s the best way to go about it
Lots of ways to clampthe transom core in. Some builders make omg clamps using 2x4s or even 4x4s and threaded rods for clamping mechanism(as above). Some jam 2x4s against the stringers to create clamping pressure at the bottom. Of course regular clamps work for the top I didn’t hesitate to use bolts, with backing blocks. I wanted the peace of mind of knowing my core was in with no voids. The holes fill easily enough.