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.

The correct solution is a function of what's in your head.  By that I mean, you need to have your problem solved in such a way that you don't spend any future time thinking about it.

I can think of nothing worse than you are at the end of the day, enjoying the outdoors in a restful moment.  Then you turn and see your canoe and your thought shift to "issues" with the canoe that occurred at the point of "delivery."  So, in terms of costs, THAT would be the what I'd seek to remedy.

dd

Yeah, your boat - your rules.  Especially if you bought it new and it's not assembled to your reasonable expectations.

I'd say it's up to them to re-fit it correctly & replace any trim to factory new.

$3k is too much to spend for shoddy workmanship and bs attitude.

Res ipsa loquitur trumps caveat emptor.


Another option, since a couple holes in the gunwale aren't really any major issue beyond cosmetic and can be filled/plugged.  This is what I would go for.
1 - They install a kneeling thwart at the location you indicate.
2 - They plug the holes, sand & seal.  Not a putty knife & wood filler plug, but an actual plug cut from the same type of wood as your gunwales.  Gued in.  Sanded flush without marring the wood.
3 - Your pick of ~$200 retail of gear.  Perhaps you want a new paddle?  Maybe there's something in the store that you've always been curious about, but never willing to spend cash on.  Now's your chance.

Congratulations!  Your canoe now has character.  Nothing has happened to it in a way that cannot be reversed so that it will not degrade it's usefulness or lifespan.

I'd ask the owner to have the kneeling thwart properly installed and to do the best he can to hide the old holes for you.  I guess I'm with those who say you should have refused to pick up and pay for a canoe that was improperly modified but that ship has already sailed.  Now you just have to make the best of it. 

If that's not enough to satisfy you, I guess other steps you could consider taking are:

Search other dealers nationcontinent-wide for a yet-unmodified Bell and if you can find one, see if your dealer will offer a refund and take yours back.  You'd have to pay to get the canoe shipped to you (and maybe the dealer would consider facilitating that step at your expense).  IMHO, this would be taking it a bit too far, but if you are truly that upset, the dealer might consider it.  If he does, you should be singing his praises far and wide to everyone you know as a dealer who stands behind his customers above and beyond the call of duty.

See if the owner is willing to offer some sort of compensatory product or service at no additional charge, such as a new paddle or an additional complimentary modification to the canoe.  Again, if he does, I'd be very vocal about encouraging others to use this dealer.

Overall, it sounds to me like your dealer is willing to meet you somewhere in the middle and for that you should be very pleased.

"I could just switch the kneeling thwart and the stern thwart around"

that depends on where that guy placed the kneeling thwart - the bow is a bit narrower, and if he cut the thwart to fit, it likely is not going to be long enough to work in the correct location  - likely, the stern thwart could be cut down to fit the bow location

it seems to me, right wrong or indifferent, you accepted the canoe the way it was - the best time to have raised the issue wtih the owner was before you picked up the boat and left the shop and came to an agreement regarding repair then - or not accepted it at all

but it is what it is, and I'd just see if the owner would have a new kneeling thwart installed at the correct location for you, and give you a few bolts or otherwise plug any unnecessary holes

I'd cut plugs paying attention to the grain and then fill the underside with a dowel. Ash would be easy. Maybe Bell would send you a chunk of walnut. If you could somehow make use of the holes make sure to seal the end grain very well and always give the holes extra attention when you oil 'em.

Then I'd find out exactly where I wanted it installed and do it myself.

Picky? You paid for a pristine new boat and you should have a pristine new boat but it doesn't sound like that's possible. You still have every right to be a prick about it. Question is, is it worth it? Did that kneeling thwart and installation cost extra? $50? Doubling that seems fair compensation just to get it settled and done with. Unless the bit they used was dull and/or the hole isn't clean, wanders ... then you bought a scratch 'n dent factory second. 

A very good question indeed. You know already me thinks, the golden rule.

From the business owners perspective I would want you to ask just what you did here. Expensive boat for him to up and replace which he seems wiling to do if he could. That says a lot about his character.

You asking these questions says the same for yours.

In most cases that will lead to a good outcome once the discussion happens. Maybe you need some other things he has or maybe you will get the forever discount on any future purchases.

I never forget the customer who realizes mistakes happen to all of us. None of us are perfect and we all have bad days. As do those who we hire to work for us. Reasonable folks can be tough to find in this day and age.

Like wally said a few holes in grand scheme is not so bad. You could put screws and nuts through them and the only one the wiser would be you and another Northstar Owner. You could also use the holes for dring mounts.

Your questions made my day. 

True that, Wally.

You're not picky...your boat, your rules.  But since you paid for it....me thinks it's now your issue.  Fill the holes and chalk it up to experience.

As soon as you paddle a few BW trips, the gunwale marks will look great compared to the scratches on her bottom.