Grant Fritchey shows that Query Store commands kinda-sorta overpower recompilation hints:
Now, no matter what value I pass it, the RECOMPILE hint is effectively ignored. I have the same plan every time (in my case, the London plan). Ah, but is the RECOMPILE hint ignored? In fact, no, it isn’t. If I capture the extended event sql_statement_recompile, I can see every single time I execute this procedure that it’s going through a full recompile… which is then tossed and the plan I chose is forced upon the optimizer. Every time.
This tells me that if you were using OPTION(RECOMPILE) to get around nasty parameter sniffing problems before, and if you go to Query Store, and if you force a particular plan to get around said nasty parameter sniffing problems, then you probably want to update the query to get rid of that OPTION(RECOMPILE) in order to prevent unnecessary plan compilation work.