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Join Date: Feb 2010
Location: Monument CO
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If timing is aligned properly then frequency response should follow and vice-versa. Fourier tells us they are the same signal whether expressed in the time or frequency domain. I am not sure how you are determining "perfect time alignment". Time delay and phase shift in the system make it (highly) likely that different phase shifts will be required at different frequencies to account for things like crossovers, physical distance, interaction with the room, etc.
The quick answer is that I would adjust for best frequency response since we hear changes in frequency response more readily than transient time events. Our ears, and brain, integrate the signals. That said, I always check impulse responses, and even with just frequency response you want to make sure you aren't wasting a bunch of power trying to feed a null.
Note time alignment also changes the relative phase, all of which impacts those peaks and valleys you hear and measure.
"After silence, that which best expresses the inexpressible, is music" - Aldous Huxley