In other questions, such as "How to properly update git on mac?" it is implied that Apple Git isn't as good as using separately installed versions of Git. What are the downsides to using Apple Git?
There are currently no downsides but there have been times when the Apple release was behind and missed useful changes.
The only downside is that it is not the latest version and so missing new features and bug fixes (and probably some regressions).
Xcode 8 includes
git version 2.10.1 (Apple Git-78).
Latest source release on git home page is 2.11.1 but latest maintained build is 2.10.1