May I answer your question? I do... both. Or, I try: batter and reso heads heads tuned usually a fourth apart, and my drums tuned, drum to drum, starting at the bottom, the same fourth difference. The tough one is the floor tom.
With new heads, I'll start with them tuned the same and leave them be, and then, as they wear in, tune them (tension them, actually) back into a fourth separation between heads by bringing the batter head up, usually (ten lug snare drums are harder to tune this way).
Now, I have a close friend, a true pro drummer, who tunes them the same, and then simply detunes one lug on the batter head to get the fourth differential.
I play jazz and pop, no heavy metal or such, so my tuning techniques are probably quite different from many. And I've always enjoyed Joe's approach, using traditional sized drums with a small group. His touch was marvelous, as was his sound. Of course, there are some* who said he didn't hit hard enough!
hardbopmans' comments are right-on.