I honestly think it is a matter of flow. Spelling out numbers is more intended for an audience you expect to read what you are writing whereas writing out the numeric forms is more for skimming. At least I have noticed that it is easier to skim through a passage that has numerals in it. They stand out among regular letters, and make them seem more important than the rest.
"Three days later." looks better than "3 days later." There is something about numerals that starts to seem rather like you are reading someone's chat message. If this is text on a note that a character is reading, the second option makes sense. Numerals for dates -such as years- makes more sense as they are much more laborious to read when written out, and can tend to take away from the flow of the story. "It was in 2018." reads better than "It was in two thousand eighteen." The numerals also give more indication of what is being spoken of. The second option could just as easily have been a reference to the amount that something had originated from.
In the same vein I agree with you that measurements make more sense as numerals than as written words because the number measurement is frequently followed by a letter based indication. With two letter indications for measurement one can get lost in the other as the reader moves through the text. "I filled the cup 5 ml." does not get lost as easily as "I filled the cup five ml."
I hope this take on it helps you.