I might have Henderson explain it at some time - it was process of elimination - he had met some of Mamba's other clones and knew they were childish and rather stupid. Mister Alexander was neither.
Asabi was certain the soul transfer had actually taken place which meant that two of the three possibles (Superman, Lois, Lex) had transferred and Henderson already suspected that Lex hadn't made it - the two in the canisters were moving around when Lex was killed and it was they he was threatening to destroy.
Therefore the person in Henderson's office was either Lois or Superman and he wasn't acting much like Superman. Lois no doubt had 'tells' that Henderson noticed in Mister Alexander as well.
