You can home any axis in any direction you wish and still have the machine coords zero position correct. For example on my mill the table moves to the right and to the front, this means the tool is at the left back which in turn means the X is correct but the Y is not as it is at its max positive movement. The way to get round that is on the Homing and limits page you put a Home Off value of the travel of that axis. This then means when you home, instead of the Y axis showing Zero for machine coords, it shows the travel of your table. On my mill the Y axis travel is 400mm so when I home the machine coords DRO shows it is positive 400mm.
Hood