A theory by me. It's also a long theory, apologies
When 001 gets sent into the upside down (he looks horrible and probably needs skin graphs) he finds the Mind Flayer. It's implied that this didn't happen right of the bat, though. He finds the Mind Flayer and shapes it into it's iconic spider tornado monstrosity thing. But the Mind Flayer was already a thing and probably was the apex predator or 'over lord' of the upside down. It also probably already had telepathic powers because, let's be honest an oddly shaped soot cloud isn't ruling anything unless it has powers.
So 001 finds it and it's implied in the show that the Mind Flayer is the main antagonist and the one behind it all. But I don't think that's the case. I mean, there's a hive mind, that implies that someone's in control right? No, not necessarily, the definition of a hive mind is 'the collective thoughts, ideas, and opinions of a group of people (such as Internet users) regarded as functioning together as a single mind. ' but then there's a hive mind in terms of colony insects, where one is in charge.
OK, I'm going on a tangent here; but I don't think that 001 has complete control over the Mind Flayer and it doesn't have complete control of him. More likely that they are both in charge of the hive mind.
Think about it; as a living organism, it would have the primary instinct would be it's own survival. And if it is naturally telepathic (my theory hinges on this), it would probably have the instinct to control others for it's own protection or otherwise. 001 one the other shadowy tendril is a human who has been recently betrayed and his thoughts are probably brimming with rage and vengeance. When 001 shaped the Mind Flayer I think he left a mental impression on it, and the Mind Flayer left a psychic impression on him. Now the Mind Flayer can display human emotions like anger and wants to get back to the 'Right Side Up', but I don't think it understand fully who 011 is and what she did to 001, but it understands that to get revenge on 011, they need to get out of the Upside Down.
Also, think about the vines 001 connects himself to when he curses people. The vines are connected to the hive mind and therefore the Mind Flayer. And I think that's how to Mind Flayer affecting 001. It's like a power booster.
TL:DR: joint 'custody' of the hive mind between the shadow monster and 001. Because the Mind Flayer is also a semi-intelligent being. When 001 shaped the Mind Flayer, he left a psychic impression on it that gave it the desire to get out of the upside down, and 001 also was effected by the Mind Flayer, and whenever he goes all floaty in the attic to curse people and he hooks up to the vines, it is amplifying his powers because he is directly connected to the Mind Flayer. Because the entire Upside Down is a hive mind.