I have ordered a VMM860AG video modulator and a MMTS20 stereo encoder, I have a few VMM600 modulators with the MMTS20 stereo encoders and I remember having to defeat the audio pre-emphasis by moving an internal jumper, as outlined in the instruction manual. Do I need to do this in the VMM860AG as well?

No need to open up the VMM860AG, the VMM860AG has a switch on the rear panel that will allow you to select “FLAT” pre-emphasis.