cutting out silence/crowd for an upload or to fit on CD is OK in my book. however, i do think part of this hobby is archiving as well as it is educational. i think part of the whole point of a txt file with source/location/etc is that if someone likes the recording so much they can go out with the same equipment and knowledge and make a similar tape. just like we should with any EQ/amplification/track splits/gear description/mic config/etc, we should state what exactly we did in the text file so the listener that does care about such things has an accurate "idea" of what happened that night.
for the record, i keep the whole master file and FLAC sets uncut, then to burn to CD it depends on the artist and show. if the whole show fits on a disc ill just leave it but if its enough of an issue i remove unnecessary tracks. when tracking, if its just a minute or two of silence/tuning i just leave it at the end of the track. like someone stated above, thats what the skip button is for. however, if the artist has a "story" segment that takes up significant time or really long tuning, i just make that a separate track that way i (and the downloader) can decide what to do with it after the fact. its really all subjective, but thats what i do.