we allow the stove to run as needed to satisfy the thermostat and leave the settings alone
Yes, that is exactly what I do. The timer settings are, by my way of figuring, the way to set how much heat the stove will make in "pilot" or "standby" mode, ie the minimum size of the fire at all times. The stoker setting (length or dots) controls only how much coal feeds into the fire when the stoker motor runs; for the last few years, once I assemble and set the pusher, it won't get fiddled with again at all 'till the end of the season.
That being said, I adjusted the pusher stroke in the fall so as to keep an inch or two of ash at the end of the grates whenever the Mag is running full burn, and my timers I adjust periodically (for a very small fire in the early and late season, and for a somewhat larger fire during winter). Right now I'm at 4 on, 13 off to maintain a 275 minimum surface temp for now.
Then, when the thermostat calls for heat, the controller overrides the timer so that the stoker will run constantly and build a full fire until the thermostat is satisfied. I use an off-the-shelf digital program job from the local hardware store and it's great in my book. With the screwy weather we've been having in PA this year (50 degrees one day, -15 wind chill the next) the thermostat has kept the house right on temp better than I ever could if I was adjusting timers & settings all the time.
I also run the combustion blower full-time, the burn quality is better, & I've installed a rheostat to control the blower output instead of using the restrictor plate. Hope this helps!