It eradicates anything with mutations of any sort. My understanding is, if you have been exposed to enough radiation to change any part of you, even on a tiny level, it would kill you.
As a result, this would kill… pretty much everyone in the wasteland. Survivors would be members of the Enclave, citizens of Vault 101, and… the list pretty much stops there.
The wasteland is full of people who have been drinking irradiated water and eating irradiated food their whole lives. They’re the children of those who have been living in the wasteland, as well, and could have inherited some form of mutation from their parents. And if they haven’t, they’ve more than likely developed their own in their time alive.
The modified FEV that President Eden gives you is designed to eradicate everything that isn’t pure humanity. Yes, that includes super mutants and feral ghouls, but it also includes regular ghouls, and every civilian who’s been drinking primarily irradiated water every day of their lives. It’s designed to reboot humanity, to get rid of every bit of impurity.