Looking through my recent Cleric build, I've noticed that the Optional Class Feature of "Harness Divine Power" has a use box that is not linked to the Channel Divinity feature of the Cleric Class. This is strange, since it says it expends a use of your Channel Divinity Feature. Shouldn't those be linked so players don't assume they're separate features that have their own, unconnected uses?

They are linked but also separate. You have to expend a use of your Channel Divinity in order to use Harness Divine Power, but Harness Divine Power can also only be used a certain number of times per day which is why it has its own use boxes.

The number of times you can use this feature is based on the level you’ve reached in this class: 2nd level, once; 6th level, twice; and 18th level, thrice. You regain all expended uses when you finish a long rest.

I suppose I'm just wondering why clicking one box doesn't auto fill the other box. If they're linked, but also separate, the refresh rate of one being per short rest (Cleric's Channel Divinity) and a Long Rest (Harness Divine Power) should be what clears them up, right? If one is clicked, and you only have 1 use, should not clicking one click the other so new users don't think they have a use of each instead of one use to use between the two options at low levels?

The rest buttons aren't smart enough for linked but also separate. Short resting will clear out the Channel Divinity tickboxes, end of. So linking them would throw off the count.