I'm not sure if that reply was directed at me or not, but that's precisely why I think they were looking at the "problem" backwards. The original proposal was something along the lines of:
1. I Add-Package NUnit.
2. This prompts the user asking them if they want to install the VSIX. If they do, this will cause a reboot in your scenario. I'm also not sure how this could avoid the prompt if the VSIX is already installed. Then there's versioning questions.
What I'm suggesting is this.
1. The user installs my VSIX. Of course this will require the reboot, but that's normal and harmless.
2. The user creates a project (item, etc.) using my VSIX.
3. My VSIX uses nupack to ensure the necessary packages are added to the project.
This seems more natural for most things, and will have fewer management issues with versions, etc.