If you bypass it, does increasing the bass/treble at lower volumes still make it sound nice? Can you even crank them far enough to do so? If yes, then this is probably the best way to go, because the loudness circuit isn't even a factor above 40-50% volume.
If it's bridged, you affect the entire volume range. Instead of tapering off as you approach halfway, it's 100% boosting, so you might have to turn down the bass/treble to compensate. Anything over 50% is even worse because now it has a loudness filter when it never did before, and turning down the bass/treble may not be enough, or may not be the right kind of compensation because the loudness circuit boosts different ranges than the bass/treble knobs and breaks differently. Just try it both ways and see which one sounds better for you.