I think his alternate costume was completely superficial, there for the sake of having an alternate.

As for Armageddon, well, the fights in the intro are non-canon, and considering the timeline has now been changed, I don't think who he was with matters anymore.

Something that bothered me about smoke, in deception.

He was tied to Noob Saibot...

Not only that. He was put in such a position to make room for Darrius, instead of being a solo-character.

Darrius?....DARRIUS!?

Something that bothered me about Smoke in Deception is when you knock him off the falling cliffs,Smoke's scream sound just like when Turbo Man (Ahnold Schwarzenegger) lost fuel in his jetback and fell back down to the street.

Ok, to clarify the story stuff: Yes Smoke was cyborg throughout that part of the timeline. No, he isn't ALL smoke, even as a human. He did malfunction in the Netherrealm during Ashrah's ending because part of his goodness clashed with the evil of the realm, HOWEVER in MKA konquest bot Noob & Smoke were in the Lin Kuei temple located in EARTHREALM so we can assume that Noob regained control of him there.

Ashrah's ending didn't actually happen. According to her Armageddon bio and the fact that Noob is still running around, Ashrah killed somebody else instead of Noob to ascend out of the Netherealm, and got to keep the sword with her.
So Noob never really lost control of Smoke throughout Deception.
A version of the moment where Smoke malfunctions because he's "having trouble adjusting" probably did happen somewhere though. See, some of the storyline Smoke was meant to have didn't make it in as a consequence of sharing his bio and ending with Noob and not having enough space for it, but it's still in the Krypt somewhere.
Notice how in the picture in Ashrah's ending, the malfunctioning Smoke is wearing his alt costume, the one that looks like a regular cyberninja? That moment was depicting his transformation, the point where his nanobots run wild and turn him into his primary costume form.
So because it was the evil energy of the Netherealm infusing/corrupting him that caused him to transform, Nano-Smoke is technically a "Cyber-Demon". (It could also have something to do with his true nature as an Enenra coming out for the first time, even though that wasn't revealed until MK9)

Noob and Smoke attacks Taven and Sub-Zero,Taven and Sub-Zero defeats them and after that Taven gets out of the lin kuei temple and Sub-Zero reprogramates Smoke to be a good guy again and planned to do the same on Noob,but he escapes. Because of Sub-Zero,Smoke is with Forces of Light in the Armageddon intro.

Smoke rules, but he is strange in 3D MK phase.