Encounter.reason: "Reason the encounter takes place, expressed as a code or a reference to another resource. For admissions, this can be used for a coded admission diagnosis."
Encounter.diagnosis.condition: "Reason the encounter takes place, as specified using information from another resource. For admissions, this is the admission diagnosis."

The distinction between reasonReference and diagnosis.condition is unclear. The names suggest one may be a prior reason and the other a conclusion, but the definition text reinforces their similarity.