I think you've nailed it DD.  When I take a look at my beauty it's really not that big a deal.  I think I've been getting hung up on principle and as any lawyer will tell you, don't go to war based on a feeling.  All I really need is a replacement for the actual kneeling thwart since, as Mad Mat pointed out it's current location makes it too short for where it needs to go.  Making the switch won't be a big deal and my gunwales are anodized aluminum so have a couple of holes with bolt and grommet won't even be noticeable.  So yeah, it'll have some character and I'll be fine with it.  
The guy I bought the canoe from is a decent sort but very disorganized.  This particular BS is only part of a much longer story and if there had been any other dealer in Ontario who handled Bell canoes I most certainly would have gone that route.  What I didn't say, which I found more than a little irritating, is that in his mind repairing the boat is tied to me using his outfitting services for my Wabakimi trip.  The truth is I'd rather be clear of him and besides I don't need an outfitter, I was able to do all that myself.  However, in the end he relented and offered to pay up to $75 for any work that needed doing and I'm sure that will cover the cost of new thwart at least.  So, in the end, not too bad, just annoyed at the very shoddy level of service.
Should I have checked over the canoe before I paid for it - you bet.  But they were running behind in getting it set up for me and we were therefore in a rush to get to Atikoken with a massive storm blowing in before the ranger station closed etc., etc.  But you know, I'm not sure I would have noticed anyway.  It's hard to visualize paddling a boat when it's on land.  I assumed that they knew what they were doing but that's got to be on me.
Anyway, in the end, all will be well and I do have the boat of my dreams.  Thank heavens I didn't wait another year.