You need to be more specific, which company and what did you pay?
If its JLCPCB or any other low cost vendor, as mentioned, nothing to do about it.
No this is not "industry practice" for any high quality NA PCB vendor. They will call you before making any modifications, or if they see anything unusual.
Oh, they touch up on your gerbers, for sure.
Standard is removal of silkscreen from bare copper. Solder mask slivers are removed. If you order PCB from the assembly house, they might change the solder mask expansion on pads. They will routinely change paste masks.
Recently I received boards, where they removed tenting from all vias, when I carefully placed them in strategic locations, to pass a certification. That's when I lifted the phone and started shouting with them about who the hell they think they are. We scrapped the entire production batch.
My other favorite was, when our purchasing guy asked the PCB assembly house to replace the board designator name on the gerbers, with something else. Because they had a different name for it in the ERP system. And I have a schedule drawing stamped by a notified body, that these are the gerbers, and we cannot change it.
Its a good thing that he already was leaving the company, saved me the trouble of getting him fired.