This is kind of... amazing. Like, actually. Hear me out guys.
It's clearly SO fucked up right; but also, it's so sad. Like it's so incredible, desperately heartbreaking that he is so unable to really do human emotion, that he even resorts to being the most intimate, with the “flower”. He is falling in love with what basically amounts to add ag doll made our of flowers, so every time that flower would, he basically feels like his lover is dying.
But still, SO fucked up. The morality of it is really on the line. It's a plant, but if it starts eventually acting more human (which I'm assuming it's the direction this is heading) that line will get fuzzy and more transparent if this keeps progression, the more human he becomes, the more it will feel like he full on raped him... Do then we have to ask, is it off to have sex with a humanoid like plant... flower...? On top of that comes the issue of age. Is the plant old enough to consent? Surely not, at least not mentally; and he doesn't even know what consent means! ... but he looks like enough, and he technically has already not only had sex before, he was able to have more kids.
I have more but I'm too sleepy so I'll just finish this up with my theories:
1. Mc changed what ml looked like because ml absorbed mc;s seed in the first chapter.
2. MC is a plant person himself.
If I remember a lot of the things I've forgotten, I'll come back to fill this out better.