I think Scott was referring more to the design of an application than to the other choices we could make, such as what application we choose to type our letters or what side of the toast we butter any given morning.
There is a school of thought that says that if you can get feature foo into an application somehow, then do it, and give the user a choice as to whether he wants to or not. There is an alternating school of thought that says that it is better to design an application to explicitly not have so many choices, instead just doing the “Right Thing”.
Obviously those are two different extremes, and the ‘best’ program would probably fall somewhere in the middle of the curve between simplicity and extreme configurability, at least in my opinion. The way I see it, whenever an application can figure out the Right Thing, that’s what it should do. Only when it can’t figure out the Right Thing should it be configurable, and even then the default should be the Best Thing (which could be simply refusing to work in situations where the user MUST provide input).
It seems to me that this is the kind of choice that Scott was talking about (at least, that’s what it seems to me judging from the end of his post). Maybe someone added yet another lame feature request to JuK ‘because Linux is about choice’? ;-)