Hi bstone -
You are thinking about how it runs backwards. The Project when launched looks at the capabilities of the CPU/GPU it is running on and if your CPU can run SM5, the project tries to run that RHI unless you have given it a command line prompt to not do it. This is the reason that you are getting the message you are seeing now.
As far as the original issue, I would need to know a little more about how you are packaging and what message you are getting when you try to open the packaged project.
Thank You
Eric Ketchum