If I create a package using an installer that does not return 0 on the exit code and specify the installer to be launched automatically, it appears that the Packaging Tool will look at the exit code and pop up an error dialog indicating that installation failed. (If the installer is not given to the wizard and a custom install method is used the tool doesn't look at the exit code).
The error dialog makes it look like the package is not good and packaging operations should stop. I found that if the error is ignored the package is just fine.
This dialog should probably look more like a warning, probably indicating the error code returned. Although I would not be unhappy if it just stopped checking the result code.
Example Installer to reproduce: UltraEdit x64 exe installer (return code is 5 but package is fine).