Is painted shoe molding more expensive than stained shoe molding?
Well it is about the same unless you are using gold paint.   Both require a couple coats, and my opinion is nail holes easier to cover when painting.  

Also you are right in making sure the shoe molding matches trim.   It is ultra awkward when it matches the floor.  (however if it is a new floor you shouldn't have to have shoe molding at all)

My take is get a quote for just the molding from someone local - see if there is a difference.   Take it to your contractor.   He didn't do the job.   So you take that amount off the bill or he does it.   It is that easy.