I think it depends on the point of view. Sure, you can think that "I want to be with someone who is with nobody else and therefore I will leave you if you have another relationship" is limiting your autonomy. But then again, saying "I want to be with someone who won't leave me because I have someone else" is limiting theirs, too.
You can make rules which decide what the other person is allowed to do (You are not allowed to date others) or you can simply state your needs and boundaries (because I'm not comfortable with you dating others, if you do I shall leave), and that's the case in monogamous relationship, and in poly relationships too.
I think many mono people aren't interested in limiting their partners as much as their interested in finding a partner who is compatible with them, which includes a common wish to only have each other.
In polyamory, some people might say "you have to use condoms with other people". That's limiting their autonomy. Saying "I'm not comfortable fluid bonding with other people through you, so while using condoms with others or not is your decision, if you choose not to, I shall use them with you to protect myself" isn't.
One problem is that many people think of it as blackmail or a threat, when really it's just about letting someone else know how you feel so that they can make an informed decision. If I tell someone that I'll use condoms with them if they don't with others, it's not a threat. It's a fact. They might decide they prefer to go bareback with me, and as a result use condoms with others, or they might decide they want to be bareback with as many people as possible, so using barriers with just me would be acceptable to them. Either way, it's their decision and not something I'm imposing on them.
Yet, one could think it threatens their autonomy, in that their actions in regard to wearing condoms will influence whether they'll get to keep having unprotected sex with me or not, in a similar way than being in a relationship with someone else will affect whether you get to keep having a relationship with your monogamous partner or not.
It's about boundaries, and I think everyone has some of them, and we all need to decide if we're fine with our partners', or if we're just not compatible.