Regarding the Z axis, you are getting confused between machine coords and work offsets. Machine coords has the Z zero as furthest from the table and all movement is negative. However just like for X and Y when you jog down to your work you can set a Work offset zero at the surface and above will be positive and below negative, machine coords will still be all negative though and you can confirm by looking at them.
Your X and Y are correct for home position, well I say correct as in industry it tends to be the opposite for the Y but they use a Home Off value so when they home the machine knows it is + full travel. You could do the same in Mach but if you are happy with your homes that way then you dont need to
Hood