This is fixed now, and companions do not engage into fights anymore if they are commanded to stay.
I don't know if their "should I attack" checks were ever excluded with the use this command as this feature was originally coded in 2004... 14 years ago. It may be
that back then they were just frozen in place, even aggressive, and when things with the game did evolve they slowly got into moving again. Original name of the command was called "Wait here" but archives clearly speak of the use to keep companions out of trouble. So now it works in the fashion as originally intended, once again.
* "Wait here"
This commands someone to stand still until you give
him/her a permission to move again. This way you can
keep your companions out of trouble and prevent them
from going somewhere you don't want them to go,
for example not to rush into the fight.
Fixed - persists in 3.62.