i just purchased Thiel CS6's and yes i hear a huge difference when i flip the phase. I use my Sonic Frontiers Line 2 preamp to do this.
I would guess its because the passive radiator is inherently our of phase with the rest of the signal. when the woofer cone moves out to create a mid-bass hit the passive radiator must move inwards. and i think the speakers were designed so that the natural physical crossover between the woofer and the passive radiator is at a common junky room resonance node (so he could hide the absence of some bass).
When I flip the phase I like them better because the low bass hits first, but you will then encounter one resonant room node in your upper bass. And it makes the stereo image recess instead of come forward.
They would be insanely amazing if they had actual cones driven for the low bass.