The blowtrough takes more time than plain cutting, so it isn't abnormal that they charge for every started hole. Also , especialy for waterjet cutting, evey startup has a marked wear and tear on the nozzle. Again logical it costs a bit extra.
Of course, some firms will use a flat fee and add the avarage hole-cost to that making intrate designs a tad cheaper, but simple ones a tad more expensive.
So in my case the firm I work with atm uses the blowtrough cost, and that can be avoided by clever design.
And yes, there are firms a tad cheaper. But this one is only 15 minutes drive away, and they don't complain about small jobs. Even better, they have cut offs at hand in most consievable materials. Send the dxf, specify material, get the pricetag. Confirm order and 4-5working days later the stuff is ready.