For the vertical landing, this would seem to work against them, but I guess the mostly empty tanks don't dominate the considerations. Falcon has oxidizer on top in the conventional manner, as far as I know (they mention LOX feed lines going through the fuel tank).
[1] The N1 rocket had oxidizer below the fuel in every stage, apparently because they wished to use spherical tanks, and this allowed packing them in a conical shape - the oxidizer tanks are much larger.