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)

    # fish
    if set -q TERM_PROGRAM  # mac os
       ...
    else if test "$COLORTERM" = "kmscon"
        ...
    else  # tron leotards
        ...
    end

    # bash
    if test "$WAYLAND_DISPLAY" == ""; then  
        echo X11
    else
        echo Found Wayland
    fi

    if test -e /etc/fedora-release; then
        echo ...
    else
        # Debian
    fi