Why a nose?
Why does the Autobot Logo sport a nose?
But seriously, why a nose? No seriously, why have eyes (optical sensors) or ears (audio receptors), touch (finger sensors), pain (damage sensors), etc? You could also think of heat sensors and other sensory equipment.
Because from an evolutionary point of view, the more senses you have, the greater the odds you recognise a threat and thus the odds you can react to it and thus increasing your survivability chances.
So why scent? For one, it might be handy to know when you're surrounded by volatile gasses and don't want to create a spark and explode the whole lot.
Or you could use it to track stuff, like predators, or, be warned of the presence of predators (like why a lot of herbivors have noses).
Taking in of air wouldn't be as much a thing for robotnoses to get the oxygen for combustion purposes for example, they can use other vents and pumps afterall. (Yes robots, or rather, their propulsion methods might need to 'breath' or they'd choke, just why sharks, aircraft and even car engines need some sort of inlets and systems to obtain oxygen even at minimum amounts for this process).
Why on a nose? Because the further away from your own body, the more seperate it is. Why do you think the majority of these sensing things on mammals, predators, birds, fish even insects have these senses on some sort of protrusions sticking out from the head? Why near the head? Because that means the time to react is shorter, it can be navigated easier etc. So all in all, a nose regardless of shape or form, makes sense. Even on a robot.
As for how the nose would work, a compact device similar to gaschromatography?
As for the humanoid face.
Consider that you could start of with alien faces, but that they adapt that too to make it suit their purposes and not alienate people they potentially could use as puppets or something. It doesn't require much explanation: everyone knows how typical TFs have humanoid faces, everyone is accustomed to them. Rather, nobody expected 'alien' faces.
So why not? Do you question 90% of the Star Trek races look humanoid? It's always been an integral part of the Transformers series, so much it basically is a standard aesthetic: Either human face or faceplate when having a vehicle format, less so when having a Beast format. However, as the target audience is human, it'll be easier to relate to a humanoid face than an alien face. For Decepticons this could be used to their advantage, to deceive humans with their looks. Coming over less threatening than they really are.
"More than meets the eye"?
There's nothing deceptive about the Movie Decepticons: 'they clearly are the evil kind of robot', spikey, thorney, detached, etc; A very Hollywood portrayal of 'evil'. Kinda like how in Hollywood films nerds have glasses unless they turn out to be a very hot chick when they suddenly lose the glasses.
Why mouths? Mouths aren't entirely necessary, a lot of TFs have faceplates as well. However, traditionally mouths are a feature many TFs have.
So they need a function. Speech is the most obvious thing, but a stereo box can do that as well. It could be made as a surrogate thing, to comfort species they encounter through familiar features (much like why you'd use human faces), who ARE likely to have mouths. The other function you could attribute to it is refueling. Of course that could be done with a valve through the side or directly to the storage compartment as well. Still, from a biological point of view, it's a very successfull formula to use a mouth as it has adapted to many functions and has little drawbacks; mainly depending on the jaw/teeth design and articulation options on what it's used for.
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