As often the answer could be: You can do both.
If you want a natural sound you should not align them because you want the later reflections.
But if your drum sound does not feel tight enough for the music, you could align them, but maybe rather with the snare drum.
Actually, no they shouldn't be aligned with the overheads. It's because the sound arrives later in time at the room mics that you get that room (pretentious) sound. See it as the pre-delay on a reverb unit. The overheads are the most important to set up (phase, dynamics, snare dead center if you spread them L-R, etc.) The room mics are the second most important for the same reasons. You might add a high pass filter on the room mics as well as on the overheads, but send them to a stereo group first and treat them as one. Like others already mentioned though, there are no rules so you can align them or make the distance even longer. Either way, I never do this because I find that you mess things up sooner than you expect.