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.
They have some greatest hits too, like repeating that higher education tends to come with a left leaning bias. I don’t think they realize why there is a correlation between education and those politics, but it certainly isn’t what they think it is.