"Is it best to build on large unit, or stack them?"
One large one would make much better use of your magnets, and your wire... and it would probably cost less.
Lets say you have 48 magnets to work with...
Ill assume its a dual rotor design but that doesnt really enter into it. But if it were...
with 48 magnets you could have 24 poles on each rotor. Any single coil would see 24 poles going by per revolution... and - for the sake of simplicity well say its a single phase machine with 24 coils.
If you broke that down into two machines, on the same shaft - and also single phse, then youd have 12 poles going round per revolution, and youd have 12 coils in each alternator.
both cases involve the same amount of magnets and the same amount of wire. The first case, you have twice the number of magnets going by each coil... so you'd have twice the power if you build 1 big unit as you would from two smaller ones on the same shaft.
The only other consideration in my opinion would be alternator diameter... if for some reason you had a limit of alternator diameter in your design then stacking units would make for a smaller dia machine, but doing so would assure a more expensive, and probably much heavier unit.
Best use of materials is to build one machine, not stack them.
And I'd disagree about the idea that redundancy is good for reliability in this case... if half your alternator failed, you'd have a serious mis-match beetween the prop, and the alternator, and it might overspeed and blow up - or.. at best, you'd have to take it down and fix it anyhow.
"What are the cog issues with multiple PM's on the same shaft?"
In a machine that has no slots in teh laminates... or no laminates at all (a dual rotor design) cogging is a non-issue. If you do have slotted laminates, which is the design that perhaps makes best use of the magnets, then... having multiple units on the same shaft could reduce cogging if they are appropriately offset. Folks do this sometimes with the F&P washing machine motors to reduce cogging.
"How many magnets/coil asseblies would be best for a rotor assembly that is 20" in diameter?"
It would depend on how much power you need at what rpm. You could build quite a powerful unit from such a large disk if you wanted.