Erin Stellato explains why enabling Query Store requires the plan cache be flushed:
I’ve had two comments recently on my blog about Query Store causing the plan cache to be flushed. There was a known issue related to the plan cache flushing after Query Store was enabled, but this was fixed in CU2 for SQL Server 2016 SP1. So I did some testing and here is what I think is causing the confusion:
When you enable Query Store, which is done with an ALTER DATABASE SET statement, the plan cache for the database is flushed.
Now, before anyone writes up a UserVoice item, understand that there are several ALTER DATABASE SET commands that cause the plan cache for a database to be flushed. For example, taking a database OFFLINE causes the database plan cache to be flushed. That one seems intuitive, right? So why is the plan cache cleared when you enable Query Store, or change one of the settings? To ensure that new Query Store data is not lost. This relates to the internals of how Query Store works, which aren’t essential to dig into, the point is that this behavior is known by Microsoft and expected.
There is what I’d consider a documentation bug around describing what happens when you enable Query Store, but the fact that the plan cache gets cleared makes sense.