For other setups you can probe a single axis at a time in any order, and if need be, adjust the origin as needed, e.g., if origin is at the top of the stock, but you want it set relative to the bottom (say if using rough cut lumber) you would:
probe the surface the stock is setting on for Z only
jog up from that origin so that the machine is where it should be at the height of the surface of the stock