There are a lot of minor differences, but the biggest difference is that you're able to be completely independent of the system python install. You bundle a complete python interpreter, all libraries needed, etc.
The user doesn't need to have python installed at all, and if they have 2.x instead of 3.x or 3.3 when you're expecting features that are only present in >= 3.5, it's no issue.
This may sound trivial, but it's a _huge_ deal, particularly when you need to deploy something that runs on multiple different OSes and versions of OSes.
Other than that, the "directory full of libs, binaries, and code" approach is a lot easier to package into something that will work well with the native package manager (e.g. an .msi for windows, etc).
