A countersunk hole is a trivial and completely standard operation. Are they plasma cutting them or something?
Your choice is:-
a) they continue to manually finish them
b) you have them manufactured using a different process
c) you don't use countersunk screws
d) find another vendor.
Its also possible they don't want to do a 2-op process. Note the lip on the back, to do that and the countersink would usually require manually flipping the part. But most places will simply charge you a bit more and get the job done.
I'm assuming here they are making the entire cover piece. If the piece comes pre-made and only the holes are cut, then there would be no excuse.