You raise some excellent and practical points.
However, it is not as difficult as you suggest. Once done, only basic maintenance is required. Each operation is confined to a separate enclosure. The coining room is the only place difficult to control, so ISO Level 4 or 5 might be the best that can be expected - once cleaned, surfaces sealed, and air flow is controlled a vacuum flush would be done each day. Struck coins go immediately under filtered compressed air onto protective carriers. The real "clean room" (level; 2, >100 μm per meter^2) is packaging which can be done in small vacuum chambers, with renewable sealed surfaces, decontamination of holders and robotic handling (as is currently done at West Point). [Multiple small chambers allow quick isolation of Q/A problems and also electrostatic environment cleaning with minimal investment.] I also recommend dry nitrogen sealed inside the capsules, if possible.
Notice that I omitted inspection. That comes after encapsulation. It is more efficient and much easier to maintain cleanliness if exposure time is minimized and transfers from one operation to another are minimized until the coin is safely under seal. Industry already uses surface imaging to detect contamination on surfaces, so this is a current technology, and not overly expensive. This is not really a human occupied clean room, so there is limited access, minimal open space. In a TPG, the original gov capsule should not be opened, but inspected for coin condition, then inserted in the company's holder. This completely avoids the chance of TPG contamination, and clearly points to the place of manufacture if any problems occur in the future.
Now this means a few bean counters will go hungry. But most of the cost is up front capital. Maintenance need not be costly, if it is well designed and integrated into the business workflow from the beginning.