In my haste to get the projects working, I added a database reference to the current project. I would build my project and reference the generated *.dacpac files when publishing. The problem is that every time I built my project, the referenced dacpac file would overwrite the generated dacpac file.
Results from this problem - I noticed that my "DeployType" variable wasn't referenced anywhere, which struck me as odd because I use it in my Pre and Post Deploy scripts. I also started noticing that my dacpac file in my build folder was out of date, even after a successful build.
Workaround - do what I have done otherwise - replace all instances of CurrentDatabaseName.dbo. with just dbo. in all SQL files in the project. This also includes the various forms that this can take:
Once I replaced all of those references and rebuilt the project successfully, my publish actions started working again. My Deploy scripts were included. I didn't get mysterious warnings about my variables not existing.
There may be a different way to work around self-referenced database objects within SSDT, but until I come across that, the workaround is to remove them from the code and not to just add a reference to the current database through a dacpac file.