Re: GENERAL CURIOUSITY...Would a boat with a soft or rotten floor have any chance sin
Cracks can be either cosmetic & not structural or as you suggested 'caused by hull flexing' which then might indicate rotted underlying structure. Hard to say w/out pix.
It is now starting to warm up in most of the US & parts of Canada, so the dry dock starts to get less frequent visits as guys start working on getting their own rigs ready for the fishing/boating season. Many have already started using their boats.
No idea what color wood was used on your boat, so dry reddish wood isn't meaningful beyond dry. Poly resin typically has a red or green tint to it, so that may be the cause of your reddish wood too.
Having little other then this to go on:
Unless you core sampled the transom by drilling some holes in multiple areas on the transom, and got NO indication of damp wood, a positive motor 'bounce' test is not proof of a sound transom.
Your friend that builds boats didn't think you should core drill the transom?