The FDA/USDA argument may be a valid one. Say someone came in right before you with a bag of tainted grain...could you please...? How'd you feel now?
1st: to the OP.. why not ask someone that can answer the question... like from the shop you got that statement from..... If it's a real answer a manager will be able to say for sure.. and a full explanation of why they can not mill outside grains might go a long way to restoring your faith in that shop. (vs listening to HBF user guesses and conspiracy theories.. See mine below
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2nd: the point quoted above... makes sense, and whether is USDA regs, OSHA, State food handling regs or some other.. I bet there is something that states their mills can only be used to mil food grade grains... what's to say what someone brings in meets that standard? Or as pointed out above, tainted, moldy, whatever grains? Leaving the store the liability risk when others after get sick..
or the regulatory body inspects or otherwise finds out that shop is milling "unknown" products in that food grade only certified mill...then shuts down, fines, requires them to clean, sanitize, have the grain room tested, inspected and certified again for food grade milling operations.
My very local HBS MIGHT mill some grains I brought in personally...very small one man shop, and a personal relationship kind of deal...
I would not expect Austin Brew supply to do the same.. that is a business first.. a few vocal employees have made that clear..Good enough supplier, and mostly good folks working the floor.. but I doubt my brought in grains are getting into their milling room.