Snapper assumes that your system is “formatted with btrfs or some other snapper compatible filesystem”. I’m pretty sure that this means that that your root directory is mounted from a btrfs subvolume.
So all you need to do is setup btrfs at install time and then configure Snapper. You should consider mounting /home from its own subvolume. That way you can roll back the system but keep all your files.
There are a lot of other things to consider when setting up btrfs, so make sure you read the docs. (A lot of the config can changed at a later point.)
Just want to point out that, while it’s a mess in practice, there is a correct place for these files and the problem is that many applications ignore it. Configuration files should be written to an aptly named folder in ~/.config/ (or more precisely, in $XDG_CONFIG_HOME which is set to ~/.config/ in most systems). ~/.local/share/ (or $XDG_DATA_HOME, respectively) is for user data, which is different from config.