The LT app note is probably referring to subharmonic oscillation present in power supplies with current mode PWM controllers and with duty greater than 50%. Voltage mode controllers do not have this problem. However, current mode controllers have a single pole response in the line and control to output transfer functions which is easier to compensate for with the compensation network. This is as opposed to a double pole transfer function which is present in the voltage mode controller. Current mode controllers can be operated above 50% duty by applying slope compensation to the the current signal.

The 24 volt would probably be the simpler implementation since you could benefit from the single pole response of the current mode controller operated below 50% duty. An additional advantage is that the input current would be much less and therefore much smaller IR drop on the input wires. The only disadvantage I see is the control resolution is less at a low duty cycle.

For tutorial on power supplies please see:
http://www.truepowerresearch.com/2011/02/power-supply-tutorial/

Bob Stowe
President,
True Power Research, LLC
www.TruePowerResearch.com

Thanks Bob!  That is some interesting detail.  I ended up going with a 24V input solution.  I'll have the hardware back in about a week so I can test it out.  

Z