No, Jang Gun has been in control the whole time until now when Overlayer took over. My read on the situation is that Yureka considers Overlayer to be the 'real' Roto now, ever since Jang Gun basically turned the 'character Roto' into an AI.
So when Overlayer appeared at the end of the chapter, Yureka recognises 'Roto' even though it is actually Overlayer. Does that make sense?
But that's just my guess though. I haven't read any further yet, hopefully it'll be clarified in subsequent chapters. Sorry if the translation has been confusing, I'm trying my best to decipher everything from machine translations, so it's possible some meaning or nuance may get lost in the process.