I am curious if you can point to some article about this being a universal.
Classifiers are a common example; words are often taught with classifiers (in most IE languages, gender) but you pick up words in reading or speech and automatically absorb the appropriate classifier even if not used, from other syntactic agreements. Japanese of course has a richer set than gender.
In another case: German, how you compose compound words (and far more interesting to me, how you read unfamiliar ones at a glance rather than parsing them as a student would) uses rules that just "feel obvious" after a while.
You a fast learner. It usually takes me several years of daily, primary use of a language before these kinds of things are intuitive.
Then again, Japanese adjectives don't behave very much English adjectives, keiyoushi (-i) conjugate much like verbs while keiyoudoushi (-na) are basically nouns with syntactic glue tacked on.
But as you mentioned, as far as I understand, the ordering is much more about emphasis than some set rule - to put it with some contrived conversations:
A: I saw a big blue ball B: Eh? It was a big RED ball!
vs
A: I saw a big red ball B: Eh? It was a SMALL red ball!
then either ordering could sound natural in context. But I'm not Japanese so I can ask my wife later if that's really the case.
https://ja.wiktionary.org/wiki/%E3%81%8A%E3%81%8A%E3%81%8D%E...
Basically, there is a short list of common adjectives including ookii and chiisai that have special 連体詞 forms ending in -na.
Though Indian languages derived from Sanskrit have simpler rules and the adjectives are roughly in the same order as English (but the endings have to match the noun).