[Ferret7446]

There are various options:

You can make forks or branches. Perfect for separating your work specific or private configs

You can use a filter like https://github.com/darkfeline/qualia-go

You can use a shell script (stored in the same git repo). You need you run an external tool with dotfile managers anyway, a shell script gives you more flexibility and doesn't need an extra dependency which might break at an inopportune time. The last thing you need is your dotfile manager breaking when you're setting up a new machine (ask me how I know)

[uasi]

You can, but forks or branches need constant merging or rebasing (and sometimes conflict resolution) for each one. Clean/smudge filters are fiddly to set up correctly and almost certainly require shelling out to another program, which could break. The second-to-last thing you need is your hand-rolled solution breaking on a new environment. If and when you need several advanced features that a stable dotfiles manager already covers, why roll your own?