Stuart, I have not read the entire thread, but you have obviously done a huge amount of research. (I've been playing for 45 years, and cannot say that I've handled 200 total OOO or OM sized guitars in all that time. Impressive). After all that, the Santa Cruz OM seems to be "the one" for you. Having one that "speaks" to you is worth a lot.
You are right to be concerned - but not paranoid - about the low saddle. 1/16" of exposed saddle is fairly low. That may simply have been the way the previous owner had it set up, for super low action. Take a straightedge and sight along the plane of the frets. If the line hits in the upper third of the bridge (not the saddle) then the neck angle is probably OK. Best to get an opinion from a good repairman that you can trust, though. If you are getting a really good deal, then the cost and hassle of a neck reset is not insurmountable, as long as the guitar is priced accordingly. FYI, my custom shop J-40 Martin needed a neck reset after eight years, so it happens even with fine instruments.
[I can't understand why someone would want to sell such a nice guitar unless they suspect imminent problems with it].
People sell really nice guitars all the time without them being lemons, or with impending problems. Sometimes it just doesn't fit. For example, once I hit age 50, my left hand no longer liked 1-11/16" necks. As a result, I have sold all the Martins in favor of Taylors with 1-3/4" necks. Playing a Martin neck for 30 minutes leaves my hand aching for the rest of the day. But I can play any of my Taylors for hours without any pain. A little dimension change and a different shape makes all the difference.