When I'm done tuning my kit, the toms sing definite notes. I tune by tension, but it will correspond to a note when I'm done. Not sure which notes. Same tensions on each tom, size doesn't matter. Like Abe said, the individual tom sizes handles the pitch separation.
Yes and no. Great answer right? I aim for perfect intervals not a perfect note, been using a tune-bot to dial those in but it depends. On a 4-piece I wouldn't bother at all, just tune the 2 toms till they sound their best. However atm I play a 6-piece and getting all those toms near perfect takes awhile and without some reference its damn hard. So atm my set is in perfect fourths from bass to smallest tom, then my snare is purely tuned by ear. Bringing the bass into the intervals really helps to make the kit sound cohesive.
I tune with the greatest speed and accuracy when utilizing an outside reference pitch that isn't effected by whatever adjustments I make to the drum. It takes me much longer trying to arbitrarily even out the lugs because whichever lug I use as a reference invariably changes as I make adjustments to the adjacent lugs. Eventually, it can be done, but it seems like a lot of unnecessary working in circles.
With an outside reference pitch, I can take a more direct route to getting all the lugs even. Not to mention the convenience of being able to consistently reproduce any tuning by simply keeping track of the notes used. It makes it easy to try out different tunings and still be able to return to the one you liked best with minimal effort. It's also much more accurate than drum tuning tools like the drum dial, or all the various tension/torque keys that I've seen.
I tune to the shell and let that be the deciding factor. The only reason I may fudge that a bit is to get them sequentially sounding correct for the amount of toms that I'm using. For my toms, I try to get the batter and resonant heads as close to the same pitch as possible. The snare and bass drums are always just to my liking without any thought to the actual note that it will be displaying. I've been doing this for years and have yet to find a better alternative.