I like it tracked separately as I think song track timings should be timings of music, not crowd noise.
In addition, it gives folks the option to delete it, not burn it etc if it means space savings.
I only include banter as part of a tune strictly if it's a meaningful song introduction, as I feel it adds to the listening experience of that tune, preferably only if it's within a reasonable amount of time before the tune starts. Any other non song specific related banter I leave at the end of the previous track.
There's something to be said for expecting the music to begin instantly or almost instant of starting a track (thus my belief of having an intro/tuning track). I hate firing up a show, kicking back and waiting for the tune to begin when I could have skipped the band walking out on stage/tuning.
2 cents.
EDIT: I strongly disagree with deleting the encore break. The show should stay in tack. It's all about the experience. I did this once but it was only with the 16 bit version, and won't do it again.