Is there where things are getting confused: "because having only one member/owner, they are exempt, or whatever, from such requirement."

There is no Exemption. There is "the right form." It goes somewhere.

"He can't put LLC A as a schedule C because LLC B is the intermediary that owns LLC A."

The non-partner LLC that is a Single-Member Entity, is Disregarded, or "pass through." If LLC B is the single member of LLC A, then LLC A's info goes on the LLC B filing, which is the concept as "disregarded."

"I hope not because LLC B's return as well as the individual's has already been e-filed."

Uh-oh.