Well, the role of duality was never played up as far as it could have been. You found the same thing with "Jem" in that regard; she would flirt with Rio as Jem, and then date him as Rio. It's no wonder the poor guy had issues, and looked at a certain way you realize that Jem was extremely deceptive and lied for no good reason - why couldn't Rio have known? Well, that's because that is where 1/2 the drama came from.
Now, it's the same for He-Man and She-Ra. Neither series would have been as interesting dramatically if the concept of "secret identities" hadn't been introduced. For the same reason Teela, Randor, and Marlena were kept out of the loop with He-Man, and the similar situation She-Ra faced. For She-Ra I can imagine it was more important, as it was a tactical advantage in the middle of a war, but it seemed that Adam was more of a hinderance to He-Man than anything else.
So, to answer your question, I don't believe there was a rationale per se, I just always bought the whole "it's for their own protection" idea. But when looked at rationally, it does make you wonder why they bothered changing back and forth at all. It's not like there was ever any indication that their transformation was somehow time limited, so one presumes they could have just remained in that form had they wished.