According to most sources, the Starship Mk.1 had its LOX main tank (not talking about the header tanks here) on top and its main methane tank below. But it seems the SN1 revision, and all subsequent versions, have the exact opposite arrangement: CH4 on top, O2 at the aft.
I thought you usually don't want LOX tank at the bottom to avoid having some fuel going in a frozen pipe through cold LOX, and that you want to keep the denser part (i.e. CH4) near the bottom – rather than up top – for stability.
Why did they change this? To my knowledge, very few rockets have the LOX at the bottom; it’s even rarer to find an arrangement where the fuel manifold goes through the LOX tank. And it's the first time I’ve heard about the two main propellant tanks being swapped in this fashion.