A Copernican View of the Turntable System

The fact that results differ slightly with the top down suggests air-borne effects,

Not necessarily. If the structure-borne feedback is resonating through the metal base of the P3 (and those 'isolating' springs can often be a happy conductor of resonating frequencies) and into the motor and/or platter, closing the lid can often form a 'capture chamber' being filled with the release of the feedback into air-borne frequencies.
Sprung decks like the Linn Sondek can surprisingly be the most prone to structure-borne feedback.
Looking at your 'System' page, I suspect your floor-mounted rack is the limiting factor. Mark Doehmann of Continuum stated that it took $30,000 of engineering to provide a floor-mounted stand like his Castellon with the same isolation as a wall-mounted shelf.
Suspended wood floors such as yours, are extremely difficult to isolate from structure-borne feedback.....and in Japan, with the seismic activity constantly providing Dertonearm's micro movements.....it should be avoided at all costs.
Any chance of you trying for a wall mount........just to experiment :^)

Halcro,
I don't have suspended wood floors. They are poured concrete with a thin fake wooden flooring cover. The rack in the system page is old. I haven't added pics in a couple of years.

The P3's springs are actually surrounded in an oil solution inside the rubber casing. The resonant frequency of the isolation system is set to be 3-4Hz. The effect is quite different to that of a normal suspended table like a Linn or Thorens. Other P3 owners might attest as to the isolation system's effectiveness.

I don't doubt that if one tried hard enough one might be able to create a 'capture system' as you propose. But the happy effect of mine is that closing the lid while playing often has a salutary effect, and never deleterious.

In Japan, TTs rigidly coupled to wall mounted shelves would be just as affected as rigid floors, like mine, with earthquakes. However, earthquakes/tremors are not the only thing causing building structural resonance, especially in cities. And not just in Japan.

T_bone,
Is your concrete floor 'suspended' or cast on the ground?
A suspended slab can often pose problems due to dynamic movement and deflections.
It's true that seismic movement is hard to protect against but most other external influences (even in big cities) can be minimized especially by wall-mounting.
The de-coupling effect of metal brackets combined with wood-based shelving cantilevered off masonry walls works in all but the most complex of situations.
SOUND

Suspended. I don't worry about whether my floor will flex though. I know it will. Earthquakes affect the sound because the building shakes (for those not used to them, earthquakes can be 'noisy'). Having had a setup on the ground floor (concrete slab) before, I know it will move too. That's life in the big city...

Unfortunately for you, seismic design entails making very flexible structures......especially at the joints.....those between column and beam, load-bearing wall and floor.
They are designed to move significantly......virtually like a hinge.
Structure-borne feedback in these conditions is almost a given.
I now understand your problems :^(
Air-borne feedback is very rarely a problem despite what you believe.