Then she meets Jun and inevitably gets sweeped.

He can't keep getting away with this!

Yet, she shows none of the signs, does not react to what she should react to, and reacts to what she shouldn't.

You look away, and when you look back it's the same person surrounded by corpses. No build-up, none of the signs, none of the usual triggers happened.

Or you look away, and when you look back it's someone else, except you never looked away, and it's just there, but it's not the same.

That's a interesting way of looking at Motoko. I mean, we know who she is and how she uses her Gamer meta-knowledge and Cold Blood to maintain her persona while on the job, but she can appear utterly incomprehensible to others who don't know any better. She's chill and even surprisingly merciful on some occasions, like with the Valetino's during her latest gig, then turns into a psychotic killer the next day with very little explanation. Then, when the slaughter is done, she plays music and smiles like nothing happened. That's discomforting.

I wouldn't be surprised if some of the characters in the story privately suspect that Motoko is a high functioning cyberpsycho like Smasher, albeit an unusual variant as you said - I can definitely see Wakako in this camp since she sometimes gives Motoko gigs, like stealing the car of the dude that wasn't paying her, to see if she "snapped" yet.

The weirdness perception will only get worse when Motoko finally goes full borg, an act which is infamous in the ttrpg books and in-universe for its huge Humanity loss...and acts completely the same as if nothing happened. We know about Adoption points, but obviously no one else is aware of it.

Motoko: "Choom! Behold my awesome new chrome! Isn't it so preem?!"

Judy: "Um...wow...you look...normal?"

Motoko: "Thanks! I was given a few options on new body types and faces, but I decided to stick to my original appearance. This prosthetic body is the best! I woke up a day ago and I already love it!"

Judy: *Shocked* "...Wait, you switched out your entire bod...weird question choomba, but how much of your original meat is left?"

Motoko: "Eh? I think it's like...four percent? Basically just my brain and a little bit of my spinal cord. Everything else is sweet cyberware baby."

Judy: *Horrified* "Four percent!? How the fu...are you okay!? How are you even functional right now!? And you only woke up yesterday and you're walking around like nothing happened!?"

Motoko: "Oh come on, it's not so bad! Honestly, I feel...so awesome. Like I was always meant to be this way. Best two hundred grand I ever spent!"

Judy: "I don't know how I feel about this..."

Motoko: "You should get a new shell too Judy! Give up the weakness of the flesh like I did and embrace the comforting strength of steel! Your ghost will thank you!"

Judy: *Thinking to herself* 'Oh right, I forgot she was nuts ever since we first met. Of course she feels dandy. Why am I even surpised?'