No, changing the tags doesn't affect the FLAC fingerprint (signature of audio data only). It will affect the wholefile .md5, though, so you don't want to change the tags after you have created a torrent. The torrent would reach 99% and you wouldn't be able to seed it correctly.

If you don't have a complete setlist, you could just not tag them. Use a filename like this for all the tracks: pearljam2007-10-10d1t01