I don't see any difference between the 2, unless you have one of those tanks with a 5 inch sand bed (I have a 1/8-1/4 inch sand layer - which shifts around and leaves some 'bare areas'. I noticed no change when I went from a deeper 1-2 inch bed to the current one. When I did it (the transfer) - I used new sand, used 1/2 'new' water and 1/2 'old water' from the other tank. I believe that I added the small amount of sand, then 1/2 the old water first, then whatever rocks, fish, etc I wanted to transfer - and then put in the new water.
If you're talking about starting a tank 'from scratch' using a bare bottom - that will also depend on what kind of rock you're using (live vs dead) etc. The volume of the tank, etc. Also whether you're adding some of your old inhabitants. If so - I would consider adding a top quality bacteria, maybe adding some of your old rock, and my guess is that you will have no issues with cycling at all.
PS - have you thought of just having a 'little' sand? with some bare? It isn't going to hurt anything - and to my liking, it breaks up the bottom of the tank some. Cleaning is the same as a bare tank, etc.
