Not at all, you made a valid point, that's why I mentioned the alternative, that is, still use the subout but use the front knob to level match. To be 100% sure you should measure the output voltage with a decent meter or at least play a tone and use a spl meter. As you mentioned yourself, turning the front knob to maximum should do the trick, as chance is good that when it is at maximum the output will be the same as that from the main preouts, but I am just not 100% sure.
So back to the 100% sure option, you would have to use two Y-splitters (one can work, but again for 100% accuracy you need two). That way, you can feed both the power amp and the sub. Luckily you SB12-NSD has separate left and right RCA input, otherwise you would need a 3rd Y-splitter.
IMO the best solution is to do the AB comparison without the subwoofer, then all you have to do is level match the two set up.