I don't think you are over thinking this, some of the other respondents may be. You have 2 thermostats, both of which "make' when the temperature of the medium they are measuring exceed their set point. The freezer thermostat is sensing the temp of the air in the freezer, the other controller is primarily sensing the temp of the outside of your fermenter. Since the compressor will only run when both controls are calling for cooling one of the controls is redundant, but the two are NOT working against each other. The reasons for adding the extra controller are twofold, you are only concerned with the temp of the beer in the fermenter and not the air temp in the freezer, and freezer temp controls, especially in inexpensive chest freezers, are not capable of maintaining the temperature range you desire. Since both controls must be calling for cooling for the compressor to run, and you want to control this with your add on, then you want the freezer temp control to always be calling for cooling. I doubt that it really matters what you set the freezer temp control at as long as it is in the "on" position. Most freezers even on the highest temp setting are below 30 degrees, but you can determine that rather easily before you put valuable beer in there.
I think you might be better off once you have fermenting beer in there with the sensor NOT controlling compressor operation off of the temp of the outside of the fermenter, but rather the actual air temp of the freezer. Remotely monitor the temp in your fermenter AND the temp inside the freezer, and lower the set point on your controller, if necessary, by the difference between actual beer temp and your desired temp. I think you'll get less overshoot and temp fluctuation this way. I will spare you all a long, drawn out attempt to explain my reasoning here.
Good luck.