It sounds as though your setup adjustments might have reduced some cartidge resonance. I’m thinking that was likely part of the problem.
And in answer to one of your questions, yes, sometimes subsonic noise is actually pressed right into the grooves. It can result from multiple steps of the vinyl manufacturing process. It can also result from warps but that is a problem more often associated with stable balance tonearms, such as some uni-pivots, as their tracking force changes when they traverse the warps.
So there’s many factors that can lead to woofer pumping, but only one ironclad solution: a rumble filter. It will only be a detriment to the sound if that is your expectation. For every one who claims they alter the sound, there’s probably a dozen who claim otherwise.