I would use nix home manager for this. Home manager has basically three separate layers. The ability to install nix packages for a user, the ability to generate config files, and special modules that combine these things things as an easy way to manage popular programs (like vim or tmux or something). You could probably just stick to the config file generation (see the xdg.configFile module).
A big downside is that you will have to install the basic nix package manager to get home manager working. You don’t have to use it to install all of your software, but it will still need a /nix and a system daemon for home manager as far as I know.
nix doesn’t play well with container environments
I’m not sure what this means. What specific things are you trying to do with containers and nix?
If you don’t want to install a bug, complicated piece of software just to manage dotfiles, maybe you could consider Ansible? I know some sysadmin types who keep their local machine configs in Ansible. It has some nice bonus features, like deployment over ssh (nix can do this too btw).