One of these rules isn't even true. There's that stand with a mind of its own in Part 4, right? The one that kills its user and then becomes someone else's stand. So I guess that's two rules.
Cheap Trick and Holly's Stand aren't really completed stands, that's why they kill the user and don't obey them. They don't have enough power to tame them. Which is weird because the architect guy had enough strength to survive being pierced by the arrow, while Koichi didn't. Part 5 spoilers:
SCR and GER are shown to obey an order from the user than directly obeying the user, but when Polnareff pierced himself on the farm he didn't sleep like everything else, because he still had a way to control the stand, unlike when he died.
I don't think it was ever shown a stand being hit by a non stand weapon, but I might be mistaken. Sex Pistols versus Green Day doesn't count because the medical instrument there was to show us
chocolatta cutting himself
.
Superfly, Strength, Wheel of Fortune and arguably Thoth can be seen normally because are made from real stuff (the pylon, the small boat and the old car).
When the user has an automated stand or a colony stand, it seems that the effect on the user only works when they're attacked directly, or in case of colony stands it could also be possible that you have to damage all of them to damage the user.