Sitefinity Project Manager vs. Sitefinity SDK EmptyProject S

I've been using the Sitefinity Project Manager to deploy Sitefinity instances to my workstation, per the installation guides. I just stumbled on the EmptyProject sample in the Sitefinity SDK, which appears to be more up to date, and uses the NuGet package manager for all requisite project references.

I am much more comfortable with this environment. Are there any disadvantages to using the up to date, NuGet managed codebase hosted on GitHub, vs. the codebase that the Sitefinity Project Manager deploys to the file system? What is considered best practice? Why are the two projects apparently out of sync?

Thanks,

Matt

p.s. Just realised, I posted under our shared account. Oh well.

Update

For anyone interested, Sitefinity got back to me through email and directed me to Creating a new sustainable setup of Sitefinity 8.x. Seems mostly comprehensive; doesn't answer all my questions, but does explain how to set up Sitefinity 8.x for a comprehensive SDLC.