Regarding XKCD 927 (that should be a word in the dictionnary), I use the include mechanism to split configuration files, and do not fear to generate configuration files whenever I want to write "echo example.org >/etc/myprog/server".

For instance my /etc/mail/smtpd.conf for my indicus.z0.is node:

name = indicus.z0.is
include "/etc/mail/smtpd.common.conf"
include "/etc/mail/smtpd.mailer.conf"

If I had more than 2 VPS, I could generate this file. Making use of the various existing configuration file mechanisms permits to make the situation really not too bad, instead of piling layers on top of others.

Adding layers is how you end up in atrocities like https://manpages.debian.org/jessie/exim4....8.en.html

OTOH, when program entirely lack a layer of "configuration format", let's be free to add one!

Qemu for instance, full command-line. Or pure-ftpd: a filesystem-based format just like the one you described (on debian)!