it basically comes down to personal preferance. To prove one way is better then the other, i believe is pretty impossible. Both bare bottoms and sandbeds have their bonuses and drawbacks. Personally I feel deep sandbeds in the display is dangerous. But I like to have a sand bed regardless for astetics. A shallow sandbed is easily cared for and adds buffering capacity.
The reason I asked why you have a 6" sand bed in your refugium was mainly trying to figure out what the basis for it was. Because its too shallow to have any de-nitrating properties, and much deeper then needed just for bio filter. As long as your not getting any detrius settling on the top of the sand, it should be safe enouph. Basically you dont want the bacteria living in the sandbed getting suffocated. vacuum the top during water changes to ensure this.
RDSB's I actually like. I run one on my system and since starting it, I have noticed a great improvment on all around stability. IMHO if it is set up properly, big "quotations" on the "Properly" they can be a huge benefit to a system, and maintain their effectivness for years apon years.
Most unexplained tank crashes are blammed on deep sand beds...i feel mostly because of ignorance.
In the end, I think this cyano "cycle" is being over analyzed. It is what it is, any tank that isnt being dosed carbon or bacterial cultures will encounter a cyano cycle. imo its best to let it do its thing and sort itself out.