I can't really comment on the difference between AZ EQ 6 GT and the EQ6-R, but I can tell you some of my experience of the AZ EQ 6 GT since I bought mine beginning of 2017.
First, when reading different threads on this mount when I considered buying it in 2016, it stood out that there were large differences in performance of the mounts out of the factory. I decided to go for a vendor with a documented expertise in characterizing and tuning Skywatcher mounts. Since I am imaging in France, I went for PierroAstro that has a very good reputation. I discussed with them and told them I wanted a particularly good example as I wanted to do fairly high res imaging (I’m now at 0.9”/pixel). PierroAstro always checks, tunes and measures the periodic error, and at delivery I got a report with a measured PE curve showing a smooth curve of about +-7“ peak-to-peak oscillations. My own measurements of the PE has confirmed this several times. If you can get your Skywatcher mount from such a vendor I think this is much preferred than buying a mount that is coming directly from factory without any check.
I now have a permanent setup, with a RC8 on top, and if seeing permits I normally get a RMS of 0.6-0.7” on the RA, and 0.5-0.6” on the DEC. The guiding has been extremely stable since I bought it 4 years ago. The periodic error as measured from the frequency analysis tab in the PHD2 logviewer shows a main peak at a period of 480s, as expected for this mount. Below you see a particularly good guiding session, but my normal performance is only very slightly worse:
As for the “auxiliary encoders”, I quickly turned them off as they really reduced the accuracy of larger slews. They appear to “resync” the mount after large slews, and platesolving sometimes failed due to a large initial offset (PlateSolve2). Since turning them off I always has the object close to center on my sensor (Atik460ex), and platesolving always centers in 2-3 iterations to below 20 pixels. As I only image I don’t see the use of them. As pointed out they can easily be switched off/on from EQMOD.
I did also experiment with PEC under EQMOD for almost a year. It worked very fine, as I could strongly reduce that peak at the 480s period as measured from the PHD2 log. But, after long testing I could simply not see any improvement on the guiding on my particular mount, probably as the PE is pretty low to start with and guides out easily. So now I simply run without PEC.
So generally I’m more than happy with my AZ EQ 6 GT, but I would strongly suggest to get a mount that has been checked in terms of PE by the vendor, not to end of with a particularly bad example of the mount.
Mikael