SqlPackager.exe excluding users in report
https://msdn.microsoft.com/en-us/library/hh550080(v=vs.103).aspx#DeployReport Parameters and Properties

look into:

/p:DropObjectsNotInSource= {True | False}

/p:DoNotDropObjectType=Users 

/p:ExcludeObjectType=users

/p:IgnoreUserSettingsObjects

Some combination of these will likely give you the Output you want.   Search that link for the specifics.   I had a very similar issue, in that SSDT Schema compare and SQLPackage.exe generated different results