I find bare bottom just not appealing. On top of that you seriously limit the settling space for micro organisms and pods.
I would however also not go with a deeper sand bed or fine sand in an SPS system - you simply can't crank up the flow as you would want and the sand accumulates way too much gunk.
On my current tank restart I'm trying a middle way with flat rocks and "thin" layer of coarse gravel. That way you get a more natural look and space for pods to have a refuge inside the tank. The deeper sand bed and the shrimp gobies that needed it go into one of my sump tanks.
As for urchins as coraline control, I found that they also like to mill over flat corals and small frags. The damage they caused me just wasn't worth it. I keep them now in the sump just in case I need them to re-condition (= mill off the surface layer) some rock.
If coraline is a problem it can be easier controlled by
Aquilonastra sea stars (often incorrectly called Asterina by reefers). I never found them to do damage to corals and most have them in their tanks anyway.
I personally prefer the coraline though.