Polarity is definitely something to consider.
It's not clear to me if you are using two signal paths. But if you are and the polarity of one of the signals changes when you engage you distortion, it will cause the lows to thin out.
It's not unusual for true bypass pedals to flip the polarity when they are engage. IMHO, the solution is to use a pedal that does not flip polarity.
Polarity is not a problem if you are only dealing with one signal path and one sound source. But polarity is a concern when you have one signal path and two sound sources. If the amp is out of phase with the PA, many quality DIs have a phase or polarity switch. Also many decent mixing consoles have a polarity switch on each input. But unfortunately it's more complicated than simply ensuring your amp and the PA are in phase.
It's not unusual for your amp to fight with the PA because of the distance between your rig and the subs. Small subs are omnidirectional, so you are likely to hear lows from the subs coming back at you on stage. After you add several subs in line they start developing pattern control and acting like a dipole...I.E. the sound shoot forwards and backs pretty much equally.
Notice the pattern is different at 50hz
If you are in the rear lobe of the subs you're going to get a lot of interaction between your amp and the subs. Or the sound from the subs may be so loud that your amp is essentially dominated.
In this circumstance you can experiment to see what polarity gives you the best sound on stage. It takes time for sound to travel over a distance. So whether the backwash from the sub is in phase with the sound from your amp or out of phase depends on the polarity of the sound coming from each sound source, the frequency/wavelength, and the distance between the sound sources. Because wavelength varies with frequency, the problem changes as you play different notes. Sometimes flipping the polarity of one signal helps, sometimes it makes things worse, and sometimes it really does not seem matter. You may not be able to perceive a difference or flipping polarity may shift the problem from one frequency range to another.
This problem is further complicated because some audio techs will delay the subs to the back line. The idea here is to try to get the subs and your amp to work together from the audiences perspective. While this tends to improve the sound out front, it can intensify the problem on stage. From your perspective on the stage, when the subs are delayed you add the delay time to the propagation delay. Propagation delay is the time it takes for the sound to travel the distance from the subs to your ears. I.E. delaying the subs makes the sound like the are further away.
Hopefully you are getting the idea that this stuff is somewhat complicated and there are actual physics-based reasons why it's hard to deliver good sound everywhere in a room. The audio tech will generally focus on trying to deliver the best possible sound to the audience. Often there needs to be a compromise because the musicians need enough quality in the sound to do the job. But it's important to understand that if the musicians insist on having perfect sound on stage, it can severely compromise the sound out front. Often if one person gets perfect sound it's because they are taking more than their fair share of the quality.
