It's just part of what I call the config pendulum.
Simple config -> (Need to do more complicated things) -> Add override levels -> (Need even more flexibility) -> Add a Turing complete language -> (Things get ridiculous, lots of spaghetti code outside of version control. Time for a reset) -> goto "Simple config"
It's fine. I am not saying it's wrong or right. I've gone through the cycle a few times in some projects. On the other hand, think of it as your project is lucky to be used long enough to have these problems. To feel better about it think of it as a spiral. The next "Simple config" is a slightly better version of the first.
That's clever insight. If it was lisp from the beginning, maybe would be more straightforward. It's as simple as code can get, according to Uncle Bob, while still being expressive. It's no wonder Emacs still reigns supreme. Well, I am happy with Niri's kdl approach for the time being.
I like to have a simple config AND a real scripting language. That way, the UX for changing "simple" things remains straightforward (you can even add a config editor panel), while for less simple things you can use a real programming language (reducing pressure from the "simple" config to turn into a DSL).
I haven't really seen program go back from "a programming language" to a simple config format.
Emacs seems to do a pretty good job handling this with the "Customize" interface. Presents a bunch of variables the user is intended to customise in something resembling a familiar interface, then it inserts the values into the Elisp init file. Someone could use and customise Emacs for years and never really touch Elisp directly. But then, oh, those text fields actually take lists, which in Emacs Lisp is the same as taking code. Maybe you use that for a while until you get comfortable and wanna try modifying something not surfaced in "customize", where you can discover init.el, etc. Etc. It's not perfect, but to me it's really close, it's the model of progression I wish all UIs for customisation used, personally.
I've seen this expressed similarly as the 'configuration complexity clock': https://mikehadlow.blogspot.com/2012/05/configuration-comple...
I like your spiral metaphor though, since you learn some things along the way.