BBEdit 8.0.1 is out and fixes at least one extremely important bug:
When “Search Invisible Folders” is turned off for multi-file searching, folders whose names begin with a period (.) are now skipped.
Unfortunately it still seems to be impossible to script the execution of the new BBEdit Text Factories (which unfortunately makes them semi-useless).
More info here: http://mjtsai.com/blog/2004/09/24/bbedit-801/