Not used trolley without bunks, and sib is ally floor. Personally I would be a bit nervous using trolley 'out the box' as standard supports not really sib friendly.
Boat lives on trolley for the season and launch/recover in surf so long bunks more practical, and packability not an issue.
Your proposal of 2' long padded snubbers plus an extended bow support should work fine and distribute the load enough to reduce pressure points on the floor. Would recommend transom is supported on rear snubbers to take weight of engine.
Have you considered transom wheels? Very popular on here and for good reason. I sometimes use them when the surf is big as recovery is much easier.