Inverting the cones (which could still be done) would only have the effect of reducing odd-order harmonics. Cabinet rocking would not be affected since the cabinet is already set up with the active drivers and PRs in an opposed-firing setup.
I'm not sure if you're referring to standing waves with the statement about the pressure not being uniform at every frequency, but in the pass-band of the PRs the wavelengths are in tens of feet (more than 50 feet for the tuning frequency) and so I can't see what effect trying to position the PRs at the "pressure peaks" would have. At such low frequencies the pressure should be fairly uniform. Where would you have placed the PRs? Perhaps you mean something else and if so could you expand on your point?
Could you expand on what you mean by the non-linear region of operation and how tweaking the tuning frequency is going to affect this?