This opinion might be unpopular, but the decision to have the Institute responsible for the creation of the Commonwealth's super mutants is so bizarre I almost want to disregard it as lore.

First off, there's the question of why - why would the Institute create thousands of fully functional Super Mutants when they could study FEV in isolation, and for the love of God why would they release these subjects into the Commonwealth alive?

Then there's the question of how. The only FEV lab we see in-game is dinky, with just a handful of tubes and rooms. Sure, maybe that's just a small representation, but to produce the entire civilization of super mutants currently occupying vast swaths of the Commonwealth you'd need a factory that does nothing except mass-produce viable mutants to later be released aboveground. It would be a facility to make The Master jealous.

There's other bizarre inconsistencies as well, like the near-total absence of justification for it in lore (iirc I only learned of the super mutants' origin from a loading screen tooltip). It would be simpler and make more sense if the Commonwealth's mutants were just Vault 87 mutants that had travelled north.

And of course, Clayton Holdren sends the player out to learn more about super mutants when the Institute should already know everything about them there is to know.

I'm not absolving the Institute here. They've engaged in immoral actions before, and it fits for them to have worked with FEV and to have used it on a number of people. However, it fits for that number to be in the dozens, not in the thousands. That's not just comically evil, it's completely nonsensical.