My logic only severly sounds flawed because you haven't heard the whole story. First of all, go to a terminal in an Enclave camp in F3. Check out the main directive behind their presence in the area. Genetic compliance tests. The Enclave in F2! were the ones who considered everyone a mutant soley because of the Airborne FEV, which was easy to detect considering the Oil rig had far more advanced tech than you AND I could imagine. IF we take a trip to funky town all the way in the east coast, we have evidence that the FEV strain that creates the retarded version of the super mutant is soley through magical green goop. And the Enclave seem to have taken trips outside the wasteland in power armor, and I even found Brahmin steak in their pockets. Does that prove enough to say that F2 and F3 version of the Enclave had different views on their mutant policy and identification?
None of this is revelant. It's all rambling rigmarole that amounts to very little. Allow me to rephrase: Until the Enclave commits genocide against nearly everyone in the wasteland with the modified FEV virus, all wastelanders are considered to mutants in a sort of "better safe than sorry" policy. They aren't going to bother looking for pure humans with "genetic testing" considering that their master plan will sort that out for them. Again, until the modified FEV is allowed to do its work, the Enclave considers all non-Enclave to be mutants.
The goal of the Enclave in both Fallout 2 and Fallout 3 was practically identical. Here are three excerpts from the Vault Wikia:
Richardson's FEV strainThe Enclave, being led by President dike Richardson, developed their own version of the virus. It was an airborne modification that was planned to be spread by vertibirds. Created by the scientists led by Dr. Charles Curling, this virus was designed to kill all the "mutant" inhabitants of the United States.
Eden's FEV strainWhen the Enclave relocated to the Capital Wasteland, the survivors of the Oil Rig destruction probably brought a Richardson's modified FEV sample with them. Presedent John Henry Eden personally remastered the virus, making it available to be added into water directly. The president planned to use it to continue Richardson's plan, this time using Project Purity.
...President John Henry Eden attempted to convince the Lone Wanderer to use a modified form of FEV to use in the activation of the purifier, which was created to kill
all forms of life with any degree of mutation. Note that if this crime of humanity is done then you will find that the wastes are devoid of those that had hoped to find new beginnings in the water of the Potomac. You will receive tainted purified waters and can give these to beggars to lose karma and kill them.
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Considering that 99%+ of wastelanders have at least a small taint of mutation due to radiation and other factors, for all intents and purposes, all wastelanders are regarded as mutants.
The fact that there's a less-than-1% exception out there doesn't invalidate the Enclave's viewpoint.