1. In Search verify that John 3:16 and <John 3:16> produce identical results.
2. Try the same two values in Media and verify that you get different results.
This violates the principles you have drilled into us:
You can even just type jn 3:16 with no angle brackets — if your entire query looks like Bible reference, Logos will insert the full syntax for you behind the scenes.
Logos Help (Bellingham, WA: Faithlife, 2016).