Installing a second version of e.g. git, perl and or python on osx lion

Yes, you can install your own versions of the programs in /usr/local/bin or any other directory of your choosing that you place on your PATH ahead of /usr/bin etc. I do this all the time for both Perl and Git; I don't use Python so much.

The scripts that are distributed by Apple will likely continue to use the system-provided tools. Indeed, the reason I install my own Perl is so that regardless of what I do in the way of installing extra modules, I won't be breaking anything the system uses (probably). I've never run into problems, at any rate. My programs use my versions; other people's programs configure themselves to use whatever they see fit; the system continues to work.