"Stages to Saturn, A Technological History of the Apollo/Saturn Launch Vehicles" by Roger E Bilstein (also NASA SP-4206, available http://history.nasa.gov/SP-4206/contents.htm and elsewhere) is a great reference on design decisions in the Saturn V rockets. One of the things it notes multiple times is that the cryogenic propellants cause freezing problems with the other propellants.
Stage I of the Saturn V is LOX and RP1. From Chapter 7 (pg 191 in the book):
The special problem of the LOX tank involved the feed lines leading to
the thirsty engines about 15 meters below the fuel tanks. To do the
job, the S-IC used five LOX suction lines, which carried oxidizer to
the engines at 7300 liters (2000 gallons) per second. To achieve such
high rates of flow, the lines could not be bent around the outside of
the fuel tank; therefore, designers ran them right through the heart
of the fuel tank. This in turn caused considerable fabrication
problems, because it meant five extra holes in both the top and bottom
of the fuel tank and presented the difficulty of avoiding frozen fuel
around the super-cold LOX lines. The engineering fix on this included
a system of tunnels, each one enclosing a LOX line, especially
designed to carry an effective blanket of insulating air. Even so, the
warmer fuel surrounding lines created some thermal difficulties in
keeping the LOX lines properly cool. So the S-IC used some of its
ground-supplied helium to bubble up through the LOX lines, and kept
the liquid mixed at a sufficiently low temperature to avoid
destructive boiling and geysering, or the creation of equally
destructive cavities in the LOX pumps.
So on the S-I (Saturn V Stage 1), you want to avoid turning the RP-1 into a slushie while still delivering the LOX to the engines as liquid. The S-II (Saturn V Stage 2) actually has similar thermal design in its way, but the colder element (now LH2) in the stage is again stacked atop and flowed past the warmer element (now the LOX).
I could swear there's phrasing to this effect that I'm just not finding in this read, but the basic idea is that if you freeze the stuff in the lines, the rocket is done for, but if you're flowing cold lines past a warmer tank the balance of the heat transfer is likely to keep your cold lines slightly warm, and your warm tank slightly cold, and everything keeps on working.