As I understand it, if you asked for a W-9 from an independent contractor but didn't get one, you must withholding a flat 28%. The same holds true if the IRS notifies the payor that the SSN/TIN on the W-9 is invalid.
I don't know about withholding for worker's comp, though. I suspect that's a matter of state law, not the Internal Revenue Code.
I would not argue with an MSC about 2.9%. However, I would ask them, politely, for their legal authority to do so, and I would also want their assurance, in writing, that I would be covered by worker's comp.