"Could I use the mid-point voltage, fed into a window comparator, to drive my tracker motor? "
Yes, No, Maybe, plus all of the above comments!
My Picaxe 40x1 Tracker/Logger is a work in progress and has been interesting for blasting some logical assumptions.
For reference - 90 watts of panels on a tracking mount on a 12vdc system. Definitely in the toy class.
For the "sensors" to work properly, you need to sun block the East or West Sensor to get the differential voltage. I tried a pair of the typical 2-3 v Garden Light cells with so-so results. The best so far has been CdS resistive elements, as I can get a good differential reading at adequate level for the ADCs in the Picaxe. Also being small ( .25" / 6.3mm ) the block and the package is small.
In addition, the panel voltage rises rapidly in anything that resembles light and just flattops against Battery Voltage, but produces no real charge current until you get good sun. You would need to really block the non-favored panel to get any differential and that is self defeating.
You may want to look at the Redrock Green LED sensor units as an alternative or just go with a small CdS package and either a discrete component design or a PIC/Picaxe/whatever design.
I find that Gray-Days ( lots of those lately - Northern Illinois - US ) are the biggest problem and they are the days that you are trying to "Milk" the array for anything that it can produce. As I said I changed to CdS differential detect, but the current re-write is going to look at the "Sun Density" and switch to time based if the levels are not good or just go flat South if it is really bad.
I reset my panes East at Midnight, but think that I am going to change that to due South and then go East in the AM if the effort is justified by the sensor readings.
Re: Power consumption - the reason that I am looking at flat due South on bad days is to avoid a net loss due to drive current consumption ( Linear Sat Dish Drive - 32vdc run at 12vdc - takes about 300ma ). That's not much, but on some days I don't make enough charge current to justify the effort.
Over complicated - Yes - but its a test system - so now is the time to make the mistakes.
Not sure this helps.
Russ