My hunch is something more like jukukjikun, where kanji meanings are combined with a reading of the whole thing and the individual parts don’t match up (今日 for きょう, 大人 for おとな, etc.).
It just so happens that 笑 part does match up, which makes it a bit confusing.
Doesn’t it sound like 笑む with 頬, with slight sound change to make the pronunciation smoother?
Afterwards, substitute the non-conjugable part of ほほえむ with 微笑 (otherwise read びしょう)?
It doesn’t answer the question about Kanji reading classification, though. But it sounds like how Kun’yomi were made, if the substituted readings cover only on one Kanji.
ほほ is still an existning reading of 頬, and yeah, Wiktionary’s theory on the etymology of 微笑む is that it comes from 頬笑む, with the current spelling likely inspired by the Chinese 微笑 = slight smile.
But in general, ほほ became ほお in the 1946 kana reform.