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.  :o