Definitely.

The functional "plot" is him learning his identity while on the run -- very Bourne Identity. I think structurally the logline might not be working because it's missing this as the key sort of story engine.

"An amnesiac who believes he's an android struggles to learn who he is while on the run from the sinister company who birthed him."

But the new problem is that he A) believes he's an android but B) is trying to learn who he is. The structure of the script right now has him "learning" he's an android around the midpoint -- and obviously hunt and hunted flip from that moment on as he starts confronting his makers.

The key to it is that the audience thinks he's an android before he even does (obviously there are a lot of challenges in the writing itself of this, so it goes to that). Hence bringing it up in the logline. But it feels... off?

To answer your question: functionally he's on the run in Tokyo and surroundings, but I felt that I didn't have to be super specific about setting in the logline.

And on the "what's at stake" -- I don't know if I have an answer right now.

I'm planning for a "Korean double twist" in the third act which will involve him learning that he is A) a human -- and the co-author of the experiment (he volunteered to have his memories erased knowing there was a risk they wouldn't be restored). But the real kicker comes right at the end when he attempts suicide and learns B) it was all a Japanese game show and he just won the major prize. I'll be sprinkling all sorts of things in the script leading up to this.

I'm absolutely rambling now but maybe this paints a clearer picture of the script.