There are a few instruments / windows & traces in a modern FFT tool.

These would include:

IR (impulse response). Typically in it’s own window. One of the first things you need to do when measuring a digital or acoustic signal is perform delay compensation so the two signals you are comparing are time aligned. If not, youre information will likely be faulty.

PHASE. The phase response is typically in it’s own window. It shows you the time different at each frequency between the two signals you are comparing.

AMPLITUDE (SIM3) / MAGNITUDE (SMAART) / POWER (SpectraFoo Complete) – These are all the same and relate to level.

If two signals are identical in time, phase & level, you get flat lines on your instruments.