USB Type-C EMCA cable - where does the mux happen?
You have a few mix-ups here. 


Electronic Marker is connected to CC1/CC2 wires, so they can't interfere with auxiliary wires;
There is no SBU wires in a Type-C USB 2.0 cable. You will need to use a full-blown USB 3.1 Type-C cable assembly for this.
No USB cable does any MUX. Ever.
I wouldn't worry about eMarked cables at all. They are reaaly difficult to come by.