I never managed a fleet. I mean I occasionally manage up to 30 instances, does that count?
Either way, my notion about doing it properly is to have a set of scripts (ansible/terraform?) that rebuild the configuration from templates and rewrite, restart everything. Afaiu, there's no "let's turn that off by rm-ing and later turn it on again by cat<<EOF-ing", cause there's no state database that could track it, unless you rely on [ -e $path ], which feels not too straightforward for e.g. state monitoring.
(I do the same basically, but without ansible. Instead I write a builder script and then paste its output into the root shell. Poor man's ansible, but I'm fine.)
So as I understand it, these dirs are only really useful for manual management, not for fleets where you just re-apply your "provisioning", or what's the proper term, onto your instances, without temporary modifications. When you have a fleet, any state that is not in the "sources" becomes a big problem very quickly. And if you have "sources", there's no problem of turning section output on and off. For example when I need a change, I rebuild my scripts and re-paste them into corresponding instances. This ensures that if I lose any server to crash, hw failure, etc, all I have is to rent another one and right-click a script into its terminal.
So I believe that gp has a point, or at least that I don't get the rationale that replies to gp suggest itt. Feels not that important for automatic management.