Most medium size + shops should have have the tooling and expertise to do the job. Generally you will be limited to a max size based on the through hole dia.
The shop term for that process is "back spotfacing". There are tools available to do it on CNC machines or manual mills (the tooling used is different for CNC vs manual).
I answered the OP as if they wanted a full counterbore, like for a SHCS, not just back spot face like for a nut. Vermont makes both tools if the OP has to front for a tool. The Vermont tools have some advantages.
Our shop used ERIX back spot facing tool to fix the nut landing areas on our flanges.
I prefer the solid Vermont tools myself. That flip-out wing on the Erix has been a little unreliable for me - especially bad when it doesn't fold back up before retracting through the hole!
I think the reason we still have the Eriz is the fact that it has been around a long time. I too like the heavier tools.
We do most of our work on a horizontal mill. Fortunately this lets us monitor the work and tool bit.