I had this bug in the GM and it went away, but today it came back, on both a 10.11.1b MacBookPro and a 10.11.0 desktop. Mail will crash within a minute of launching. The error is:
*** Terminating app due to exception while holding database lock 'NSInternalInconsistencyException', reason: 'Cannot set MFGmailLabelStore as data source for message.'
abort() called
*** Terminating app due to exception while holding database lock 'NSInternalInconsistencyException', reason: 'Cannot set MFGmailLabelStore as data source for message.'
abort() called