Since query by _profile is not required, there is currently no way to query for MedicationKNowledge instances that are FormularyDrugs.  The only required element of the Formulary drug that is queryable is PlanID, and this can only be searched by exact match.   So, a client can distinguish a formularyDrug instance from another use of MedicationKNowledge following retrieval – the existence of the PlanID extension – but there is no way to query for them.   So, retrieving by code might return extraneous instances.

If this is a bug: One possibility is requiring support for the :missing qualifier on the PlanID search parameter.  The would enable a search:
<fhir-base>/MedicationKnowledge?PlanID:missing=false
that would do the trick.