Define a named Area for each block of components that will be added to the PCB, then set Match Pair spacing rules for within each Area, ensuring you set the Area to be used for Area Based Rules within the PCB when there.
The SCM is the master for defining the net list and the components, the PCB is the physical. There are items used in the SCM that are not known by the PCB and visa-versa, for instance a Schematic Block is not known in PCB, as Copper Pouring is not known in the SCM. This is expressed by the contents of the Technology files.
Spacing Rules can be defined for net to net, type to type etc in the SCM, within what it knows, or expects, to be in the PCB. It does not know about Areas that will be in the PCB, but these were allowed to be defined as part of the spacing rules definitions. The Area in the PCB is of course a physical area, so this cannot be defined by any more than a name in the SCM and added manually in the PCB to correspond.
For note: One way of having a named selection of components in both SCM and PCB is by using 'Group'. An example of its use can be seen in example design 'Led Display' and the accompanying Word document.