What happens when battery power is too low to move the fan and the PWM is sending out power still? Harm to fan? Harm to controller?
That could be a problem. A quality controller would use a low voltage dropout regulator to protect itself from this. The one you pointed to can regulate down to 10 volts. It could heat up below that. You will have some line loss depending on what wire you use. A battery voltage below 11.5V (just my guess) might create 10V at the controller.
Why not try the one you pointed to on eBay? It's $13 delivered. 25KHz switching frequency so it shouldn't be noisy, rated for 10A and has a power switch. I assume you already have the wires located where you want it on the wall. Did you run 16awg wire? Wires being too small/long could be a problem.