Uhhh... Are you not in control of your emotions? In addition to what others have said, I don't see the conflict you suggest. The only times I don't control of my emotions are when I lose presence of mind, such as when an emotion flares up or I'm otherwise distracted. By the way people talk of their experiences, it seems most people are like that too.
A further complication, of course, is that I often lie to myself about my metacognitive life, so I'll be angry, and I'll hold the opinion that it's better to let that anger go, but I won't actually do it because there's something really satisfying about being angry. Like when you're sad and someone is trying to cheer you up and it's just annoying and you're like, fuck off Clara, I'm brooding, and she's like, whatever.
So in those situations, that's a more prior motivation that I'm not addressing. I want to want to stop being sad or angry, but I don't actually want to stop being sad or angry.
I don't think there is any particular reason why you couldn't have that full level of continence where your opinions about how to be and how you actually are are perfectly in line. "Why aren't we perfectly motivated?" is an excellent question, but I think it's a very similar question to "why don't we have perfect attention?"
Anyway, if you're thinking more in the lines of controlling your autonomic nervous system, I don't see why it would be impossible for someone to do a sort of pavlovian jury rig where you condition those responses to thoughts and feelings. Given the fact that humans can be lied to to elicit physiological responses and that placebos and nocebos do something, it's conceivable that a particular mental framework could control the release of adrenaline or dopamine or melatonin or whatever it is, but it is questionable if we even know enough about human medicine to be able to handle that ability with wisdom.
I have often found that if my behavior and thoughts are not aligned, resulting in anxiety, dishonorable behavior, laziness or whatever, there's something I'm being dishonest about, or there is some more subtle factor I'm missing. Like being anxious because I'm intimidated, but if I recognize that, then I can sort of normalize it. It's the things like recognizing what I'm feeling and why I'm feeling it that usually make things a little tougher to handle.
I guess what I'm really saying is that I think if you're lying to yourself to fix your mood, it's probably only because you lied to yourself to get that mood. How we lie to ourselves and forget we did it all the time (justification) is probably a better waste of your time. So, you know, go
If it's not obvious, this isn't science , just what my armchair told me.
Also, gut microflora might generate psychoactive substances such as dopamine. Also, the nerve cells throughout your body might pre-process information such as touch before it even gets to your brain.