Single-column junction table - does it make sense?
In my mind I would separate the logical and physical design. Logically there is a entity type called StoreGroup. Physically, this entity type is not implemented as a table. This is OK. Often the physical design does not include all aspect of the logical design due to time constraints, priorities, performance or other reasons. Foreign key constraints, and the corresponding run-time checks, is a typical example of this. You've discovered another.

There is a cost, too. As you say, foreign keys cannot be enforced in the DB. Perhaps your application has other mechanisms to ensure consistency? As is so often the case there is a trade-off and the designer must make a judgement call.