I'm about to pull the trigger on an eqm-35 mount and it supports PEC. I'd like to take advantage of this feature but not sure if it just happens in the background?
No it does not. Furthermore ZWO has commented that they have no interest in adding that feature. So take that into consideration.
It seems there are features that don’t get added or won’t get added because they will “confuse” users.
There can always be additional options in asiair and still not confuse users. I like UI of asiair. It's intuitive and well designed, but I miss more advanced settings. Especially for autoguiding. Phd2 should really be more complete. Astrophotography is not making selfies with friends. It's serious photography. And not cheap too. Buying equipment worth several thousand eur is not piece of cake. So lacking of important features just to make it easier for masses is not the right approach. Developers have made great progress since the beginning and I'm sure we will eventually get most of this little box as we can. About pec. If you're guiding it really isn't that important. It could even make tracking worse. For unguided it might be good idea.