Not really sure I understand but will have a go.
When you reference the machine it will set the machine coords to zero if you have the Auto Zero option chosen in Homing and Limits setup. The only occasion they will not be set to zero when that is chose, is if you also have a Home Off (offset) value entered in Homing and limits.
Regarding the work coords (ie not Machine Coords) they can be set to anything you wish, if you want them to be the same as machine coords then you can home the machine then zero each axis and that will set them to the same as the machine coords, unless of course, as previously mentioned, you have a Home Off value set. If that is the case then you can enter the number into the DRO and that will make them the same as your machine coords.
Hood