As long as your sub's volume control is within the adjustment range of the auto-setup program, it'll compensate for any variances from sub-to-sub.
So if you've run the setup and the bass sounds too loud, and turn down the volume, then re-run the setup, it'll likely turn things back up to where it was before. If you think it's too loud, just turn down the subs (or manually adjust the settings in the receiver), and leave it.
Pioneer VSX-1018AH-K, PDP-5020FD, DV-79AVi
Axiom M22s, VP150, QS8s
Sony PS3, surround backs