well the reason the organ kind of get all these rows, is because of all the knobs and switches that have to fit within reach for the different organ voices.
Not entirely accurate. The multiple manuals (keyboards) are so you can set each of them to different
registrations (combined sets of pipes) and play them simultaneously. Each pipe set is represented by a stop on the organ console. So the more manuals an organ has, the more stops it tends to have.
It's up to the organ builder to arrange the stops as conveniently as possible. But over a certain number of manuals, a console can be only
so ergonomic—for an extreme example, the organ at the Boardwalk Hall Auditorium in Atlantic City, NJ:

I'm guessing that to reach those high stops, the organist must either have an assistant on a stepstool, or wait for a pause in the music and stand up on the bench. :?)
For keyboard, if everything already fits infront of you, there's no real reason to layer it.
Even if that were the reason, why not make a multi-level computer keyboard anyway—for the visual effect, if nothing else? I'd sure enjoy seeing one!