Good question, OP. I'm lost too.

If this is true, and it seems to be a fitting description, then why the heck should I destroy the whole Institute by placing a bomb to the reactor and kill all the inhabitants incl. children? As humankind-loving Preston proposed to me recently. It was my pleasure to kill the Railroad stupids and I accept fighting against BoS invaders, but I have problems to kill the Institute people.

Maybe I will reload to a save before becoming enemy of the Institute. What I would like to do is make them stop producing Gen 3 synths.

Virgil spent years in the FEV lab before finally growing a backbone. However, it seemed like it was mostly about the experiments being pointless rather than the experiments being unethical. Liam started helping Synths because it was originally a game. The Institute is just like everyone else. Most of them are trapped in their own little world with little consideration of anyone else.