They didn't know what the Master's FEV did, remember that's a huge difference between Maxon's FEV which was causing Lovecraftian body horror. One of the patients grew a tenticle out of stomach which attacked a nurse. And besides, they retrieved it to see hat it could do.
The Enclave knew damn well what Mariposa was. Just because they were holed up during Fallout 1 doesn't mean they wouldn't know how to do intelligence gathering, both passive and humint once they started taking an interest in the mainland. And besides, the Enclave was scrambling all through 2077 to button up because the storm was coming and they knew it. Records like that are easy to get lost. And besides, neither the body horror FEV or the Master's FEV is what the FEV project was designed to create. The FEV was supposed to be a Captain America serum, not a Hulk creator.
Now this DOES create a huge fucking plot hole in Fallout 3, which is, assuming they have all the databases of Vault locations, or even the ability to download all the locations of the VaultTec central mainframe in Washington DC, why not lift the Geck out, use their stockpiled resources to reverse engineer it and creating 'paradise communities where they could de facto enslave the local "mutants" and profit off their labor. OR....just create an EEP only countermeasure that they could spray over the countryside and cause the 87 Supes to melt into organic slag? And man oh man a gun that did that like the Fallout 1 & 2 plasma weapons would be tits!
But all they needed to do have 87 be mostly filled with Supermutant corpses with a few survivors eating their brothers, and the GECK went, with Autumn, still captures you as a place to find and ambush you.
That said, no one I know will defend the Fallout 3 main story. The main story is balls to the walls AWFUL. I don't want a Fallout 3 remaster over Fallout 4 because the main story is better, Fallout 4's is better, although that's like saying shoe leather has some nutritional value. I want it because the World building (locally) makes sense, the side quests are a LOT of fun, and most importantly, all the niftysettlment mechanics go MUCH better in Fallout 3 AND the modern modding scene could make this a fabulous playground.