The panel wires go to the controller input and the controller output goes to the battery wires. Never have the controller downstream of the converter, which is also on those battery wires at the power centre fuse panel end.
So yes, you can wire the controller output NOT THE PANEL output to the battery wires at the fuse panel This puts the controller and converter in parallel, which is fine.
BTW, the longer distance from battery to controller is not a concern so much for lower amps, longer charge time, but for the effect on the controller's high set point for when to stop the voltage from rising any higher. With voltage drop the controller will "see" it has reached its high set point , but the battery voltage will be lower than that. This can leave the battery under-charged.
