MSBuild and BizTalk

Question

Is it possible to specify (or override) the Deploy ApplicationName, database server, and database name for BizTalk projects? If so, how?

Unfortunately this data is stored in the btproj.user file instead of the .btproj file, and my client doesn't want to check the btproj.user files into the source control system.

(FYI - we are using BizTalk Build Generator from CodePlex.)