I use a full scale 'simulator' based on X-Plane and photo scenery to supplement my microlight student's air time. Of course it doesn't count towards their flying hours, but I only charge ground school rates so it's cheaper than flying (and not weather dependant). I've found it helps some of them learn some of the mechanics of flying and with modern photo scenery they can practice navigation techniques.
I've found some people don't slot into the fantasy and treat it as a computer game. These people don't benefit much at all. People who do slot in to the fantasy, however, can learn a lot. A big training benefit is the ability to pause the simulation and explain where they are going wrong. The biggest disadvantage is that they don't learn airmanship and lookout.
Would
unsupervised time on a desktop simulation help? I can't answer for big stuff, but down at the lightweight end of flying that I inhabit, I would say that it does as much harm as good, so you'd end up paying an instructor to correct the bad habits you wouldn't have developed if you hadn't used the thing.
They're fun though.
MB