Last Lemming, Millercarbon is correct; unfortunately, it is the turntables' interaction with the listening space. I had a similar experience with my turntable a few years ago. It was an Oracle Delphi Mk II with an SME V arm and Benz Ruby 2 cartridge. The entire setup was placed on a Target TT-1 wall mount turntable rack, mounted into the studs of an exterior wall. Oracle Audio pioneered the record clamp back in 1981. I installed everything myself, with much help from Wally Malewicz. After an exhaustive trial and error process similar to what you did, and contacting Oracle several times, it was discovered that the SME V requires a different suspension spring configuration than those typically shipped with the standard tune-up kit Oracle sells to keep the Delphi operating to spec. Once the correct springs were placed in the correct suspension towers and properly tuned, ZERO woofer pumping.
The woofer pumping occurs from acoustic feedback, resulting from the turntable suspension not being properly tuned for your combination of tonearm/cartridge, and/or your room’s resonant frequency. I know that the VPI is a "suspensionless" design; however the feet are made of different resins and polymers designed to filter out unwanted frequencies, but just aren’t doing a complete job of it. The Pioneer is even less equipped to do so. I have since upgraded to the Delphi Mk V in African Black granite, which has a platter mat made of vinyl resin concavely ground so that when the record is clamped it does exactly what the design of Millercarbon’s rig does, presses the record so that is is flat across the playing surface. You will NEVER get the same result from a record weight alone. You can achieve a similar result by utilizing a weight AND the peripheral ring clamp on the VPI; they are deigned to be used together. One other thing that may help, get yourself a shelf for the turntable to sit on that is decoupled from, instead of mass loaded to, the environment. Again, note Miller’s setup. The Black Diamond Racing Shelf for the Source is an outstanding device, albeit expensive. I am using a Z-Slab from Zoethecus (unfortuantely defunked) on top of a 1" African Black Granite slab in the TT-1 instead of the stock shelf. Yes, that’s a whopping 105 lb mounted to the wall. The Z-Slab/Oracle Mk V is supported by weight appropriate discs from Grand Prix Audio, and this has resulted in dead silence, from a turntable sitting 4’-5’ on the side wall from a F-13 Fathom sub and M-L Ascent i speakers in a 14’x11’ room.
Good luck with your journey. I hope that this will give you some direction in resolving this problem. I KNOW how frustrating it can be, but with perseverence, when it is resolved it will be SO worth it. Almost everything I play now is on vinyl even though I have similarly spent on digital for not only this one, but the other systems around the house. EVERY room has its’ own music system; it’s good for what ails ya!