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Optoisolator should help as it will keep the board power and the TEC power completely separate. It will complicate the electronics though, if you are using the original G106 housing things may not fit inside any more. By the way, there is a deeper version of G106 by Hammond, part number 1550Z111.
Keep in mind that we will most likely have to use the humidity pin for the TEC as the current TEC pin does not support PWM. Still doing tests here so don't do any changes yet.
While you are at the design stage here is another thought. The 3.3V regulator gets quite hot as it powered by the input voltage (12V). The camera actually only needs about 6.5V (say 7V to be safe) to run. If you are using separate power supplies for the TEC and the camera electronics you can power the camera with a lower voltage to reduce the heat production.
In my current design I use one 12V power supply but the camera electronics is powered by an external 8V regulator while the TEC gets the full 12V. This way some of the heat is "moved" from the PCB to the breakout box outside the main case.
Regarding the TEC designs, both are possible but I am not sure about the 2nd drawing where only a part of the hot side of the TEC is being cooled. If possible you should shape the cold finger to look something like a letter T in side view. The top of T should be square and fully cover the TEC while the bottom "leg" of T should be round and go to the cold finger through a hole in the PCB. Hope this description makes sense, if not I can do a drawing.
My current design is like your first drawing and I can get down to -40 degrees C below the ambient temperature with the TEC I mentioned before. The final temperature, of course, also depends on the size of the heatsink and the fan.
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