I can only relate to the way "I" work.
My machines use a fixed point probing for tool length offset (in G53 coordinates), I always use G54 coordinates for my work piece, and on each setup, I designate a location 0,0 in G59 coordinates to do tool changes and this location varies depending on my setup.
My routine is to home the machine, designate the location for the tool changes as desired and locate my workpiece datum. Then I save these various offsets in case of say a power failure, a crash cause I did something stupid, etc. This way, I can start over with confidence that things will be located in a proper positions.
My setup program also gives me a chance while homing etc to make sure oil is distributed properly etc and just generally check things out before doing the actual work.