orthography - Intuitive or logical way to know when to use a kanji spelling vs hiragana spelling?

A recurring theme on this site is that foreign learners of Japanese use too much kanji. Often the reaction is puzzlement that we can't "just know the right way". Native speakers literally say they don't understand why we use too much kanji:

... Why you always write things in kanji, I never understand.

Since native speakers can't understand why we do it, there must be some intuitive or logical way to know.

Is it as simple as "If the word uses any non-Joyo kanji then hiragana is probably best"?

Or is it that if we can tell it's ateji then hiragana is to be preferred these days?

Or are these just two of several factors involved in deciding?

For example, the last word this came up with for me was "まめ" meaning "blister", which has the following kanji spelling which I don't think uses non-Joyo characters but I think probably is ateji: 肉刺