There is no technical way to get away from "phasing" issues of two or more pickup positions. The best you can archive is a different spacing of the teeth of the resulting comb filter.
Flipping the pickup does nothing for pressure sensitive pickups, only for bending sensitive ones and that flips polarity and has nothing to do with phase, even if it is almost always called phase.
Two-element bridge wing pickups which connect the shield to the outer brass on both elements are pressure sensitive in the same way, but since the bridge crown presses on one or the other, the resulting signals are "out of phase" (which means if one goes up, the other one goes down in amplitude). Exchanging the shield and signal wires on one of the pickup elements would get them in phase but put the signal on one brass enclosure. (If the elements were made different, I.e. by flipping the crystal of one element only the brass of both could be shielded. But then the electrical orientation of the crystal needs to be measured and I doubt that would be done since this might be some additional work that is not that simple. I rather guess that the electrical orientation of the two crystals is by accident only.)
Phasing issues are produced by a time delay. As long as the time delay is the same for all frequencies contained in one of the signals, this can be compensated by delaying the quicker signal by the same time amount. But in case of the bass the time delays from one string to one of the two pickups is different to the time delays from a different string.
Phasing means a shift in phase, but this is a different amount of time depending on the frequency. This is possible with electronic components, but it does not eliminate the problem we have.
Since there is a great misunderstanding about phasing issues and what the typical electronic circuits do we can discuss this for years without getting away from where we are now.
If pickups and preamps would be much cheaper: the more pickups you use distributed over the top, the better the signal gets, because the teeth of one comb are filled by the signal of another comb.
That might also be the reason why a closely positioned large diaphragm mic sounds better than a smaller diaphragm mic at the same position, but I'm afraid there are a lot of other reasons that might have more influence than the diaphragm size alone.
So with a two element pickup you always get a comb filter effect. The only thing you can do is moving the regularly positioned teeth, which might sound better on one note and less good on another.
There is nothing wrong with flipping the signal polarity on one of a two element pickup. But it changes the sound. If both signals would be identical, the signal would cancel out but due to time delay and different volume amounts of components with the same frequency this doesn't happen with bass pickups.
Flipping the polarity of a mono signal to an amp also changes the sound, but can help to reduce some peaks in the feedback frequency response which can be more important to a change in sound. It can also make it worse, since it depends a lot on bass top to speaker distance (the time delay) and signal flipping and phase shift (mostly in the EQ circuits) of the electronics.
