I had motoros in a tank with sand substrate who covered themselves from time to time. My current ray in barebottom has never attempted it once or at least not that I have ever seen. He still blows at the bottom but never flaps in an attempt to cover himself. It would be interesting to add sand to the tank now and see if he recognizes the sand being there and attempts to cover up. My guess would be no because I think they only cover up when they feel uncomfortable and he is very comfortable in his surroundings. I personally think it is cognitive thought and not relying on instinct. I know I have read somewhere about rays being more advanced than your normal fish but not certain where they fall on the intelligence scale.
I agree with this as well, Now that all my rays are comfortable and accustomed to being in bare bottom tanks I do not see them attempting to bury themselves anymore. The only rays I own that attempt to do this are my pearls, They have been in my tanks for just about two years and they still tend to be quite nervous and will dart around the tank and attempt to bury themselves even thou there is no substrate in the tanks and never was. These pearls are the only ones that exhibit this behavior when spooked. My leo,henlei, p14 and motoro do not exhibit this type of behavior anymore. I do not agree with a ray being happier in a tank with substrate or stressed out in a bare bottom tank at all. There are plenty of breeders in asia and thru out the world breeding there rays in bare bottom tanks with much success, I think they grow to be use to any type of tank and adapt to there surroundings if not would they be breeding in bare bottom tanks?