The barrel being off-center in the stock isn't a big deal as that will change/vary each and every time you remove/reinstall the barreled action into the stock until you glass bed it. Just loosen the action screws and retighten while holding the barrel centered in the barrel channel.

As for the front swivel being stripped, personally I wouldn't send it back for that. Too simple a fix to bother with the expense and hassle of sending it back IMO.

Wouldn't worry about the scope base screw either - just shorten it and forget about it. Action diameter can vary a little (few thousandths either way) and it's nothing to get bent out of shape over. Most likely it's a simple case of the curvature of the bottom of your scope base being more closely matched to this action than the other so it actually sits just a hair lower rather than having a slight gap between it and the action in the center where the screws are.