The workflow that you show in your repository is really not that different from Chezmoi. If you configure a post-add hook in Chezmoi (https://www.chezmoi.io/reference/configuration-file/hooks/), you can do `chezmoi add ~/.config/whatever/whatever.conf` and have the file auto-added to the Chezomi git repo + push it to some remote if you'd like.
I was also not thrilled about the idea of shipping an encrypted blob of important secrets around. I want my dotfiles to be public, so it's much nicer when the tool I use for managing my dotfiles natively integrates with 1password. Much of the templating functionality that I use from chezmoi is specifically for pulling stuff out of 1password.
Finally, the yadm "alternate files" functionality is nice, but I didn't really care about alternates for different OSes or hostnames or whatever. I wanted some configuration for my work machine(s) and some configuration for my personal machine(s) - that's it. That's the only distinction I care about. Chezmoi made it easy to prompt for the type of machine + change the things that get configured accordingly when bootstrapping a new machine (https://github.com/cweagans/dotfiles/blob/main/.chezmoi.toml...).
Where did you find yadm fall short?