I mean, the very quotes you quoted shows that Aulus did NOT know all there was to know about souls, since we pretty much took him by surprise throughout the battle. Even if Aulus knows more about souls than anyone else on the planet, there are clearly gaps in his knowledge. So, assuming that just because Zenos knows Aulus, he should know how to use his soul to transform a host body is a logical leap - particularly when you consider that Aulus is the expert, not Zenos. Just because Aulus tells Zenos something, does not mean he'll understand it fully.
Even if we assume that Zenos SHOULD have known how to transform, there are advantages to being disguised as an Alliance Elezen. He gets to move freely throughout Alliance territory, for one, and when he DOES encounter opposition, they don't react with, "Oh, crap, it's Zenos - deploy EVERYONE!!!"