All of the AutoMate apps have one thing in common - they record realtime moves of the typical parameters that one would want to save while mixing i.e. anything affecting the audio path. What AutoMate is not designed for is writing automation envelopes in Reaper for in-box mixing. AutoMate is strictly an out-of-box mixing automation solution.
Off Topic
Patrick has another app called X32Reaper that enables use of the entire console as a control surface, with deep integration with Reaper
Plugins are totally usable on an individual track basis but because there is no Master Bus use in this configuration, there will be no plugins on the MB. That does not mean you cannot Master your mixes while using AutoMate with Reaper. There is a slightly different approach for Mastering and editing mixdown tracks and that approach is built into AutoMate. The thought being that with AutoMate, the mixing is done in the console and that with perhaps a few exceptions, the FX and dynamics would come from the console. AutoMate has no impact on the use of Waves plugins/servers.
The User Assign section has a full transport on bank C, including automation control for recording, playback and editing. Some new features have recently been added that are very exciting and allow very high resolution automation recording/editing that was not previously possible with real-time automation systems.
As a veteran of something on the order of 500 analog mixes from 4 to 24 tracks over several decades, I can tell you that with an X32, Reaper and AutoMate, mixes that rival anything done on those legacy consoles by all the big names is possible. And, because of being in the digital domain, there is no midrange smear caused by slow slew rate ICs or ageing electrolytic capacitors in the audio path. One of my hobbies is taking original tracks of famous songs and doing my own mixes using AutoMate on the X32. The results are astonishing, putting it mildly.
In another post, I will explain how to do Mastering and editing using AutoMate without using the Master Bus in Reaper.