@Tamerlane I agree with you. To me the dragonfly story is a
metaphor to Gen's mindset.
Just like Gen is keeping them in the plastic bag, he's trying to keep them to himself, with no route to escape. But the father gives him the advice that even if he wants it he can have them, but must poke a hole, otherwise they will asphyxiate.
The same thing is happening with Reiji now, he's
trying to keep him close in every way possible (being an errand boy for him and in the future working together), but the way he's doing it is wrong and too asphyxiating (just like keeping the dragonflies in the bag).
Poking a hole in the bag kinda means, in Reiji's situation, giving him some space to "breathe", but just like it happened with the dragonflies even if you try to do something for them to live longer they still die anyway.
This memory probably molded Gen's mindset that
"Even if I gave him some space, I'll still lose him. So I just might try to keep him close as much as I can and being the one to decide his destiny".
This is how interpreted his flasback.