I second that opinion regarding the reliability of the ARC with the optional HDMI on the Atom pointless if forced to go the Opt out route.
In my case though, the TV seemlessly pairs with the Atom using the CEC Protocol, enabling volume control and auto On/off of the Atom using the TV remote, which is the very convenience of the ARC and CEC systems as you mentioned, no need to have 3 or 4 different remotes handy. However, I can testify that there is slight lag not for the volume but when pressing the On button of the tv'sremote, for the TV to wake the Atom up from sleep mode. I do know though this is very common and not specific to Naim gear but rather to the CEC protocol itself ("Anynet CEC" on Samsung TVs)
However, my greatest grief and issue is regarding those sound drops that occurs maybe once every hour or every two hours.
I came back home from the office during the lunch break and did a complete reset of the TV and re-connect everything, and it worked just fine, but I did not stay enough long to guarantee the problem won't repeat once I get back home tonight to watch my favorite show.
And as you, I found the Atom to be a thrilling kit, working beautifully and driving all the various speakers I have with authority and sky-rocketing dynamic and pace abilities.
Just frustrating that one cannot use the HDMI output as intended.