guys, this is an important distinction and NOT a meaningless pedantic point.
the key thing is that, as this poll demonstrates, when you ask the question "do you leave your speakers the way Audyssey set them or do you change the settings (small/large and/or crossover freq)?" there is a tacit implication that you are manually overriding what AUDYSSEY has recommended, i.e. you are moving away from the "optimal" setting.
Audyssey however does not have any control over the bass management functions, receiver manufacturers have refused to give up control of that. The primary reason is purely marketing, in that uninformed end-users get insulted when their big tower speakers are set to "small" (this is not a joke, it's really the reason).
With respect to these settings, all Audyssey can do is pass along its measurements to the receiver, where the manufacturer's logic determines the settings. This is usually a "dumb logic" decision where they simply set the crossover as close as possible to the measured -3dB point reported by the measurements. That decision is in no way "optimal" and it's important for users to understand that. Many people implicitly "trust" the auto setup because they assume it's smarter than them and is optimizing their system, and thus are concerned about deviating from these settings (thus polls like this).
Audyssey explicitly recommends changing all speakers to "small" and raising the crossover if necessary, for example read this: http://www.audyssey.com/blog/2009/05/small-vs-large/
If Audyssey was allowed to control this aspect I can guarantee you would never see a speaker set to "large" (unless there was no sub in the system). Ideally they would be able to do what happens with the Pro Kit, where they actually calculate an optimal crossover freq which provides the smoothest response at the crossover region.
The key point of the distinction is that by changing speakers to "small" and raising crossovers, you are not "overriding Audyssey", you are in fact conforming to their recommendations. It's an important thing for people to understand so that they don't feel they may be doing something "wrong" by changing a setting after auto setup.