At least some of that is the inevitable consequence of pronunciation changing over time ("rz" being the standout, which used to sound like the Czech soft-r, but

At least some of that is the inevitable consequence of pronunciation changing over time ("rz" being the standout, which used to sound like the Czech soft-r, but lost its r-colouring) and others attempt to show an etymological relationship, which makes spelling a bit more difficult in some ways and easier in others.