I agree with you that your autonomy is threatened by the manipulations of others. But threats only sometimes turn into harm- distinguishing between manipulations you agree with and disagree with is a valuable skill.

Indeed, there's a general point that needs to be made about human interaction, and another about status, but first a recommendation: try to view as many of your actions as manipulations as possible. This will help separate out the things that, on reflection, you want to do and the things that, on reflection, you don't want to do. For example:

if a friend told me that he spent a lot of our time together thinking through ways to positively reinforce some of my behaviors, even to my benefit, I would become very suspicious of him. I would feel that I'd been treated as a child or a dog. His behavior would seem to me to be manipulative and dishonest,

Emphasis mine. The reaction- of calling his behavior manipulative and dishonest- feels like it punishes manipulation, which you might want to do to protect your autonomy. But it actually punishes honesty, because the trigger was your friend telling you! Now, if your friend wants to change you, they'll need to try to do it subtly. Your reaction has manipulated your friend without his explicit consent- and probably not in the direction you wanted it to.

So, the general point: human social interaction is an incredibly thorny field, in part because there are rarely ways to learn or teach it without externalities. Parents, for example, tell their children to share- not because sharing is an objective moral principle, but because it minimizes conflict. As well, some aspects of human social interaction are zero sum games- in which people who are skilled at interaction will lose if others get better at interaction, and thus discourage discussions that raise general social interaction skills.

The status interpretation: generally, manipulation increases the status of the manipulator and decreases the status of the manipulated. Resistance to manipulation could then be a status-preserving move, and interest in manipulation could be a status-increases move. What articles like this try to do is lower the status effects of manipulation (in both directions)- Luke proudly recounts the time Eliezer manipulated him so that he could better manipulate Eliezer. If being molded like this is seen more positively, then resistance to being molded (by others in the community) will decrease, and the community will work better and be happier. As well, I suspect that people are much more comfortable with manipulations if they know how to do them themselves- if positive reinforcement is a tool used by creepy Others, it's much easier to dislike than if it's the way you got your roommate to finally stop annoying you.