As with any dotfile repo, I wouldn't recommend installing the entire thing at once. Instead, try and take the time to read through it and select settings that you want piecemeal. You'll end up knowing what everything does, especially in the case that something strange happens and you want to tweak things.
Edit: I should note that I learned this the hard way starting out, I went backwards by ripping out things that didn't work for me/did not like, but not until after making some horrible mistakes!
As the author of this dotfiles repository, I completely agree. These are my settings, and I’m sure not everyone will like this configuration. The idea is that automating all these OS X preferences (hidden or not) can save you a lot of time if you need to set up new accounts for yourself on a regular basis.
TL;DR This repository is meant to be forked, not used as-is.
Edit: I should note that I learned this the hard way starting out, I went backwards by ripping out things that didn't work for me/did not like, but not until after making some horrible mistakes!