Sonically, you could use either 48v or 24v since the phantom adapter is stepping down the voltage to 9V no matter what is being fed to it.
Battery wise, 24v is better because it will drain your battery (or batteries) less quickly. Obviously very helpful when stealthing with internal batteries. I run my F3 almost exclusively with an external battery and when I run my at853rx's (hard wired to an at8533x phantom adapter) I switch it to 24v because why not *shrugs
Line In or Mic In will depend on how loud your source is, but I will personally say that almost all of the things we tape will benefit from Mic In. From what I've read here, the Line In is simply an attenuation (-20dB?) of the Mic In. If you find yourself stack taping a metal show it wouldn't hurt to set it to Line In to be safe, but I have done some pretty loud metal shows with my F3 using Mic In with no issues. YMMV and if it's an important show, it doesn't hurt to be on the safe side IMO.
There's lots of battery tests in the F3 thread, I recently did my own with some 7-8 year old AA Ni-MH rechargeables and I think I only got around 3 hours using the 24v setting. :/ I thought it would be better, but the rechargeables are quite old and have been used a lot. I will be ordering some Eneloop AA rechargeables sometime in the future and will post my 24v test results. I don't mind using Alkaline AA's for important shows, but the thought of not only spending money but then throwing something away for each show bugs me and if Eneloops can reliably give me the necessary time for most shows then I will use that option.
EDIT: removed some off topic thoughts on the F3 and FR-AV2, will probably post in the F3 thread. That's my bad, my mind tends to drift to many different topics!