As I use these three different tools to fiddle with my repo, am I at risk of them not agreeing on the repo internal structure?
No. The main internal structure (pack format) won't change so much it would become incompatible with older git 1.8 versions.
And you can have as many different version of Git on your computer: they are portable archives, that you can unzip anywhere.
The only limitation is in term of feature (like for instance, pushing to shallow repo, which is only possible since git 1.9.0)