@lsjames:I'd have to dig into your scenario a bit to answer this fully. In general, DAC upgrade will try the most minimally invastive upgrade strategy possible. I'm a bit suprised that it's messing with users, are you using DAC Fx 3.0 (that ships with RTM SQL 2012)?
Q: The scenario I'm thinking of is having a single SQL Server Data Tools project as part of our solution and using TFS builds output dacpac files for SQL Server or SQL Azure (i.e. targetting the two different environments via configuration and then build the dacpacs). Is that possible?
A: Absolutely. Think of .dacpac and .bacpac as a single-file deployment capability for schema (.dacpac) and schema + data (.bacpac).