OK, good job on the calibration.
In your place, I wouldn't worry about this. The temperature probe on the ATL2200 is likely a simple NTC which has OK linearity, but the analog amplification circuit needs to be properly calibrated. There may be a hardware calibration (typically a potmeter) somewhere in this circuit in addition to the software calibration you've already found.
But, as you also indicated - it's likely that Jobo included this measure based on their own measurements and aimed at correct temperature of the actual developer. I think I've read something similar about other Jobo processors, and it does indeed make sense. Given that the target temperature of the developer appears to be correct, I wouldn't worry about any of this.
Btw, at the risk of driving you crazy - what matters is not just the temperature of the developer in the bottle, but more so the developer temperature inside the tank as development takes place. Technically speaking, that is what you should be measuring and controlling for instead.