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.