For key switches, apparently they can be swapped out: Swapping out keyswitch mechanisms
The Model 01 firmware, Kaleidoscope does indeed have plugins for Space-cadet shift, dual-function keys (which, as you point out, there isn’t really a big difference in practice – SpaceCadet is I guess specifically for shift/parens, while the dual-function is a more general idea), and mouse control, including scrolling (both horizontally and vertically).
The graphical configurator, Chrysalis, is coming along (I’m one of the people working on it) and is fairly functional at this point.
I think there’s a max of 32 layers fo the Model 01 as well.
The Win/Level 3 modifier is the GUI key on the Model 01. Not sure about Hyper – in my experience, I’d just have a key shift into a layer with whatever special keys I want there.