I think the key to understanding this new SVS/Audyssey equalizer is in the intended market, for which it was built.
SVS states, "But this still affordable box is the best way to optimize any sub, even big "do it yourself" (DIY) subwoofers, virtually eliminating room factors that distort sound. Entry level customers with limited audio budgets might decide instead to just get a good current AV receiver offering less-robust correction systems to economize. No AVR-based room correction system has the sheer refinement and processing horsepower, nor can it cope with dual subs nearly as well. Leave the AS-EQ1 as an upgrade on par with any consideration you put towards dual subs, or investing in any world-class sub from SVS such as our PB13-Ultra and PC13-Ultra, or top subs from elsewhere."
Current A/V receivers with Audyssey equalization cover the entire sound spectrum while the new SVS equalizer specializes in just subwoofer bass. The subwoofer signal path is where the SVS equalizer can be inserted, which fits with an aftermarket equalizer. The bass region does appear to be the greatest benefit of Audyssey equalization. Even the Onkyo 606 with a limited 2eq Audyssey system I could hear a marked improvement in bass with the Audyssey system turned on. If you want to learn more how Audyssey works in general with A/V receivers, you can read the official Audyssey thread in the AVS Forum, which is very long. One member of the Audyssey development team (Chris) provides a lot of answers and insight into Audyssey.
http://www.avsforum.com/avs-vb/showthread.php?t=795421
One of the recurring themes is that Audyssey provides a flat frequency response through the subwoofer region and apparently a lot of owners prefer a "house curve" for their subwoofer. If you add an equalizer to get a house curve, then you mess up the Audyssey correction for the time domain. It would be interesting to know if SVS permits a house curve while still maintaining time alignment. I think that would sell a lot of people on the SVS version.
