Handling high voltage input range to comparator
A comparator running at 5V and a voltage divider will work fine, you wont be attenuating the signal in any non-linear fashion so the signal going into the comparators will work for you.

You stated the input voltage will be a range (6 - 50V) and as you said you would use a 10:1 divider, then at 50V your max input would be 5V and at 6V your max value would be .6V. I'm sure any decent comparator will be able to distinguish differences in the 10's of millivolts (conservatively). I looked over the Microchip application note you linked, The circuit shown on page 14 looks great, it provides a virtual center point so you don't need a positive and negative voltage supplies.

Concerning the power supply it seems as though your best bet would be to supply the higher voltage (6 - 50V) then use a buck converter to bring the voltage down to 5V, something like the TI simple switcher designs like http://www.ti.com/product/lm46000 would work (I don't work for TI, I just like their simple switchers). They even have an example schematic.