on the first 3.8 I owned, I would regularly trail the boat on a bunked Indespension JS09 trailer, with the engine fitted, and a bracket with a roller supporting the transom directly below the engine. It never presented any issues or did any damage to the boat. Undertook several long distance journeys that way. The engine was a Yam 20 2 stroke, lighter than a Honda 4 stroke 20.
I coud easily push the trailer around by hand with the boat on it, when on the level or a slight incline, but not on a proper slipway. The trailer was unbraked, and I wouldnt want to be trying to manouvre it by hand on a slipway by myself.
I almost never used the seat. I got a couple of floating boat cushions - the type that WAFI's often have in their cockpit, and would often perch myself on one of those in the boat. Gave a more secure feeling than sitting on something the height of the tubes when it got a little "bouncy".
When I first got launching wheels and fitted them, I would never take the trailer onto the slipway ...it was easier just to roll the SIB off the trailer and walk it down the slipway on its launching wheels.
Hope that helps.