I have done estimates for insurance repairs and it is surprising how easily everything adds up to make repairs uneconomical. For instance, if the frame is marked, a dealer will add a new frame into the estimate, even tho' it may only be a bit of damaged paint. Parts prices in an estimate are obviously for new parts, and if much of this is genuine Yam, well we all know what those prices are like. Using the frame as perhaps the worst case scenario, you would then have the labour to strip everything off the damaged one, and rebuild the bike around the replacement frame, at the hourly rate your dealer charges. Dealers will put everything on that estimate they think has been damaged in the accident, however lightly marked. There may be some room for discussion with them about what goes on to the estimate.
What happens then is that the insurance company will send an assessor to view the bike. Armed with a copy of the dealer's estimate, he will examine the machine and negotiate (or insist on) repairs to, rather than replacement of, some parts on the estimate, whilst giving the thumbs up for the rest, assuming a repair is economically feasible. The dealer will then agree a new final estimate with the assessor.
If the dealer regards the repairs as uneconomical, i.e., a write off, he might not write up the estimate in full, but simply state that in their opinion it would be uneconomical.
Well, that's the side of things I've seen first hand, so maybe gives you some idea of how the repair bill came to be so high in yours and similar cases.
I'm sure others can answer your other points.