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Google Chrome shows a smooth transition when you type something in its omnibar. It consists of a few frames of a diffuse glass-like autocomplete box before it becomes totally opaque.
It's faster than I can consciously perceive, I only noticed it because my computer froze at the right instant.
I wonder if those faster-than-the-eye improvements can be really perceived at some unconscious level.
If its faster than the eye can see then I doubt we will be able to appreciate on an unconscious level. I think that transition is there as a backup for when systems are performing slower than normal and the user needs to be informed that a process/action is taking place.
As you mentioned its about the subconscious level, if the system or application can provide a perception that a system has changed state in a high speed that it almost seems instantaneous, it enhances the user experience since it gives a sense of continuity and also informs the user about the change.
To quote this article from smashing magazine
A good transition should be almost invisible to the user. It should help the user understand where they are navigating to and where they have come from, but it should also be smooth and quick. A stall or stutter impairs the overall user experience and tells the user that something is wrong. There is such a thing as UI motion sickness, where the user gets so used to the fluidity of moving between screens that when a screen freezes for a second or two, the user feels like they’ve come to a sudden stop. It is these sensations we should avoid.
