"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