The default holy rotations will use Heal to take advantage of the Ephemeral Paradox proc when it occurs (see line 14 of the Max Healing rotation). If you equip the trinket and run a sim, you can see the Heal casts and the mana gained (but not the total mana saved, it doesn't seem to display the Clearcasting part of the proc).
Regarding why it is ranked so high, the default setup for Raid Healing sim is a very long fight, and the sim tries to go all out to get the maximum throughput possible, so small mana gains are represented as larger throughput gains than you may see in practice with more controlled ability usage. I've gotten fairly realistic recommendations with a shorter fight. I use a 120s sim for my gear recommendations and make trinket choices based on other theorycrafting sources, but mana trinket recommendations vary significantly with fight length.
Maybe experiment a bit with a few different fight lengths (either by the "More Options" dialogue on the sim page, or creating a new Boss/Script based on the Raid Healing default) until you see recommendations that fit your expectations more closely.