What benefit is there from enabling Query Store on msdb?
Microsoft enabling a feature does not mean it will be useful for everyone. For systems using some of the features can mean relying on information stored in MSDB.  In those cases Query Store can be useful.

Here are few articles about the usage and tuning  of MSDB database objects. 

msdb Database from books online.

MSDB Performance Tuning by Geoff N. Hiten 

The Importance of Maintenance on MSDB by Tim Radney where he mentioned following:


  Optimizing indexes in msdb is just as important as your user
  databases. Many times I have found clients who are optimizing user
  databases but not the system databases. Since the msdb database is
  heavily used by SQL Server Agent, Log Shipping, Service Broker, SSIS,
  backup and restore, and other processes, the indexes can get highly
  fragmented. Ensure that your index optimization jobs also include your
  system databases, or at least msdb. I’ve seen index optimizations free
  up several gigabytes of space from highly fragmented indexes within
  msdb.


I can see how query store can help in optimizing your indexing strategy and optimally querying/aggrgating/purging some of the information stored in MSDB.