Whenever you see a sustained long note of the Baroque piece, it's a sign that a long trill can sound well here (even in middle voices). Remember those Dominant or Tonic pedal points?
This idea comes from knowing that on many keyboard instruments back in the day (harpsichords, virginals, clavichords) the sound would fade as quickly as you struck the note.
So if you added a trill on a long note, chances are this note would be heard for much longer - as long as you play that trill.
Sure, not in every case you see those trills written in the score and organ sound can last indefinitely.
But it's nice to add something extravagant in that style once in a while.
Like a wig, really.