It is difficult to fight the Physics. I guess that the answer is to be happy to play up an octave or more for when we want the synthy goodness. Obvioulsy this is sub-optimal, but physics is physics, and the reality is that a sound that is not bass guitar needs to be played differently anyway. I would be happy to play a normal guitar in some situations if there was a patch on there that "just" did a good, solid, believable bass guitar sound.
Classic self-inducing GAS post from me here. On another note, I think they might have used the synth to pitch Nate's voice down a bit