Are you using git submodules? We manage 63 plugins across two different instance and four environments (Dev, Test, Stage, and Prod) using submodules. It makes it easy to pull in changes from plugins if they have a git repo.
Yea, subtree is my preferred choice too.
I have to manage a lot of instances with a lot of different plugins and different versions.
One of the important things to me is, you can give your customer access to the so custumized moodle repository without access to all the plugins. That's something you can't achieve with submodules.
Another thing I like on subtree is you have the whole history at one place and you can work with it without changing into the plugin direktory.
Personally, no I'm not - I know there are strengths to that, but for now I still have everything in its own independent repo and just use a bash script to replicate a whole site, or update an existing one. It's then easy for me to just manage that script between sites for which plugins I need on a WIP or Dev or even localhost site.