I think some bike clutches (e.g. Ducati) and most racing clutches lack radial softening - i.e. the springs that take up small differences in position, and help soften a drivetrain. They also tend to 'preload' a clutch, which stops them from rattling. Multiplate clutches (not normally used on road cars, unless they are pretty high performance) will also suffer rattling when the plates are unloaded (i.e. you press the pedal or pull the lever).
In my racing, I can fail a noise test (105dB(A)) if I press the clutch pedal, but pass it if I leave it engaged in neutral. That's how much of a difference it makes. But in gear and driving, they remain quiet, and whilst changing gear the engine/wind/road noise covers it up anyway.
Crunching gears would be hard to simulate in most cases. In LFS you can't force a gear in as gear selection is either in or out (on paddles or h-shifters), but you could add a generic 'gear crunch' noise if the clutch isn't disengaged (and the shaft speeds not matched, as clutchless shifting is possible in ALL cars [and in LFS, correctly]), or is (dis)engaged at the wrong moment during the shift sequence.
However, I think it's such a small useless thing that it can wait until gearboxes, clutches and other stuff around them are 'simulated' in more detail, which again isn't a pressing issue.