Yes, if the audio being matched is of a cleaner or dirtier amp than the amp in the preset, maybe this produces the variance. For instance, if your source is clean, and your tone match block is after a heavily driven amp, the purpose of the tone match block is not then to perfectly reproduce the 'signal type' of the source audio, i.e. to clean it up... (It's my understanding that the user needs to do a good job of factoring in what a similar signal chain is to get the desired result, and use this IN COMBO with the tone match block).
For example a synth sound can be smooth, or have a lot of distinct, amplitude-varying harmonics. If I were to try to match that harmonically-laden synth, the resulting tone match block would in theory provide allowance to let thru that sort of harmonic environment, but if there is no way for an Axe FX preset to generate a very accurate version of this quality (and ordinarily there really wouldn't be) then of course the two graphs would again be very different.
Er, I rest on my guitar case..