As far as I remember, your companions will only attack if the npcs are hostile with the exception of boon. Boon will always shoot legion on sight. You can have some decision over their actions though by talking to them.

As for the armor it does matter when and where you have it on. Again my memory may be foggy but factions can be peaceful or aggro depending on what you are wearing. You can even go into a camp with hostiles if you have their faction armor on.

Take all of this with a grain of salt though, it's been a long time and I did play with and without mods.