I do not see an obstacle why you could not run MID to yield two distinct custom packages e.g. in the following way:
1. install base Virusscan on a client where MID is installed
2. create the first custom package with MID.
3. install the first custom package on another client where MID is also installed.
4. copy the first custom package from the first client to the second client and run MID to modify that and generate the second custom package.