The 1099-Misc doesn't go on a Sched C. All earnings from the consulting operation are on the Sched C. The operation(s) that results in the Sched C is what is subject to the QBI regulation.

The 1099-Misc is a notational function, which means it is used for reporting what happened when it meets the reporting threshold. It doesn't define anything regarding the QBI. If your client made $5m from consulting, but no one paid more than $599, there would never be any 1099-Misc forms used for reporting.

You are relating things that do not relate.