I do the same thing. But I also have customized branches to work with my config. I will usually make new commits on the computer-specific branch and then cherry pick the commits to master and then rebase the computer-specific branch on top of master. This can get a little repetitive and result in my computer-specific branches getting very out of date so I wrote a bash script called git-update to streamline this process for me. Here's the code:

https://github.com/axelson/git-update