Exactly.
This was my thought as well.
Some missions although you can join if others have their honor where it needs to be and invite you, but if your honor is high you wont be able to play the low honor missions on your own, they wont even show up in your mission list.
I had been invited to a mission, I forget the name it is the one that takes you to the fort East of Valentine, well I joined from an invite but on my own the mission never came up, I later realized I had to lower my honor and that is exactly why you see the honor changing option at those stations around the map, you can also do it yourself for free like I did.
I ended up going to St Denis, climbing onto a rooftop across from the stables and sniping people and police until my honor was very low, then I went into the menu and tada, there was the mission, after I completed the missions that require low honor, I went fishing and just playing the game the way I normally play it and my honor was back up in a session.