Usually among the same speaker line a larger woofer = greater efficiency, along with slightly better bass response. Honestly, from a music standpoint, so long as the speakers in question are -3dB at about 60hz that’s plenty when paired with a sub.
The b6 is only 2dB more efficient, however, woofer diameter and surface area determines how effective the driver is at coupling to the air at lower frequencies, providing lower distortion at higher spl.
If the same xover point is used, a larger woofer will have worse dispersion off axis at the crossover frequency and slightly worse performance on the midrange.
Practically though, the differences are likely to be minor, the b6 would be a bit better at higher volumes and have better bass.
There is no reason a 5.25” woofer should have issues reproducing solid mid-bass (>60hz), especially when ported.
Major differences are found between floor standers and bookshelves, when multiple woofers or three way designs are employed.
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