Brett - what you say has merit. Deciphering phase / polarity behavior has a lot to do with the ear-brain's reference, and having the deep bass delayed does affect the overall sonic fingerprint. But keep in mind that the vast majority of speakers introduce such phase distortion at every crossover point. That global, full-range scrambling may obscure the phase picture enough for the ear-brain to stop caring, drawing attention to Thiel's polarity sensitivity. I concur with your observation.
JA - I think that Jim's passives were spot-on, textbook best implementation. And the frequencies are low enough to be out of the critical midrange area. It is solid bass. The only real compromise is the inherent phase lag of the ported / passive deep bass driver.
Brett: "They would be insanely amazing if they had actual cones driven for the low bass." That debate was real in our company. Jim began the subwoofer development project with hopes of incorporating active bass into the model 3 (4) and 5. Class D was in its infancy, and that project took further years to bring to fruition, so the model 3.6 was developed with a passive/ported bass and further models followed suit. I personally lobbied for keeping sealed bass in the model 3 with an implementation of bi-amp possibility for the woofer with a higher output woofer for the model 3 and develop a model 4 with the additional low-woofer for a sealed 4-way to fill in to the sealed 5-way model CS5. The lower-priced models 1 and 2 could use the ported bass.
Those decisions were made by Jim as CEO and Kathy as Marketing Director. As we all know most speakers on up into $6-figures employ ported bass as a cost-effective solution for deeper bass with higher output capability. But I, and it seems you, and possibly many others think that the otherwise seamless coherence of Thiels above the low bass spotlights that timing inconsistency of the ported bass alignment.