Do modern large aircraft simulators fail to properly account for what happens when you land too hard on the main gear? That seems like exactly the kind of mistake they'd want to simulate accurately.
They do, thing is the field of view is not accurate and not 3D, some simulators have a basic 3D rendering (they change the image at frame rate that it 'feels' 3D). So you need to rely on instruments to create a mind image of how high you are.
That actually happens not only in simulators: when you are used to land on wide runways, the next time you go land on a narrow one you would flare too low (and approach too low), specially at night.