Actually, Shiro being a clone makes much more sense than him being the actual Shiro.
Operation Kuron? Come on. That’s pretty obvious a play on Kuro, black, aka the opposite of Shiro, white. Has Shiro’s memories? Was tested on? Pink fluid? Longer hair than actually possible? In Galra clutches and in the prisoner rags? It makes no sense that it would be the real Shiro.
Regardless if Zarkon was trying to gain control of the black lion, Shiro was the Black Paladin. Shiro is the one she was currently fighting with. She would fight for and protect Shiro regardless if Zarkon wanted to take control. She would teleport Shiro somewhere safe - with the rebels who rescued Matt. She didn’t respond to Shiro not because Keith is the “rightful leader” but because that’s not her Shiro.
The Shiro that’s with the paladins right now is literally Kuro. Or in this case, I guess Kuron. He’s a weapon created to destroy voltron from the inside, and he probably doesn’t even know he’s giving the Empire all this information he genuinely thinks he’s the real Shiro.