I thought the same thing (at first).  But now, my AdrenaLinn III has a permanent place just before the PitchFactor.  The pitch detection hasn't suffered, even when I'm using the more extreme "dirty" amp models.

If you're running in stereo (as I do), there's no other logical placement.  The ADR III is mono-in, stereo-out.  And that leads to some amazing effects.  For example, simple stereo panning in the AdrenaLinn acts as a synchronized "voice-switcher" for the Diatonic and QuadraVox modes.  It ends up sounding like very complex finger-picking, especially using random panning.

Tremolo, filter, and "arpeggio" sequences, as well as some of the other stereo effects, are really inspiring when followed by the PitchFactor.  When you get a chance, check out some of the FX beyond the amp models.