TL; DR
This dependency-based planning is a common feature of project management in general, and isn't limited just to agile methodologies. However, it seems very applicable to the agile planning issue you have outlined.
Think Dependencies, Not Composition or Inclusion
An epic can have a dependency on another epic or story, so in reality your dependency diagram might look more like this:
+------------------+
| |
| Common Story |
| |
+--+------------+--+
^ ^
| |
+------------+-----+ +--+---------------+
| | | |
| Epic 1 | | Epic 2 |
| | | |
+------------------+ +------------------+
So, rather than trying to put the same story in more than one place, or trying to decompose your epics in a way that feels artificial, you can simply make the common story or epic a prerequisite.