If it were me, I would NOT bond the transfer switch legs together because you may forget and than someday wire for 240. If it were me, I would bond the generator produced 120 to BOTH the red and black wires in the flex cable and than feed this generator produced 120 via this flex cable to BOTH legs of the transfer switch (i.e., black wire to one leg and red wire to other leg). I would also have CB between the generator 120 and the bonded red/black wires. Make sure the CB is of proper rating to protect the wire gauge you are using with the assumption that ALL the current will be carried by only one wire (i.e., red or black).