Will there be an update that will feature an harmonic minor scale?
It's included as of version 2.3.0. (Current version: 3.0.0).
I plan to run it through my effects loop. Is this recommended?
Many here do. A quick search through the forum will give you an idea of what to expect.
I also have a reverb, flanger, and phaser that I run through the effects loop. What is an optimal order?
I might go with the PitchFactor – phaser – flanger – reverb, but experiment with the order. "Conventional wisdom" usually dictates Dynamics – EQ – Drive – Modulation – Time Based effects in a series configuration.
Pitch detection devices work best toward the 'head of the line'. I have several pitch-shifting 'boxes on either side of my drive / distortion modules. The PitchFactor is after the Drive, and before Modulation and Time-Based effects.
Keep in mind that these are generalities; open to debate, preference, and desired effect. But there are underlying practicalities and variables to consider in any routing.