The first is that I have a habit of running `git add .` when I'm working on source code, and as a result I have accidentally added my entire home directory to the bare repo more than once... Easy enough to undo but a bit inconvenient. `dotfiles add -u` is the safe option, or just be explicit about which files you are staging.
The second issue is the 'branch per machine' approach, which I do use. I have two machines I use regularly, and a third occasionally. There are some bits of config (e.g. for vim) that are shared across all the machines, while other bits are not. If I use one machine for a while, then I end up with lots commits that I need to cherry pick when I next use another machine. Depending on how long it has been, this can be a bit of a faff.
Finally, because there is no clear mainline branch, you have to pick commits to/from any of the branches. If you are undisciplined like me, then this will leave you with a 'three way ahead and behind' scenario at some point.
Anyway, I like the approach overall. If anyone has a suggestion to ease those pain points I'm all ears.