Electronic – Can conformal coating help against high-temperature environments if the chips heat up as well

Maybe, maybe not, but I'd ask why you are not correlating hot chips with power supply currents, and why you're not putting a temperature sensor on the heatsink. If the thermal path from the die to the heatsink is impaired you'll get a different temperature differential between the die and the heatsink. Likewise, if the chip is drawing more current you should be able to predict the final temperature of the die based on normal thermal behavior. And measuring the heatsink temp doesn't require a dedicated contact sensor: a temporary one will do, or a non-contact IR unit should work, since the emissivity of the heat sinks should be pretty uniform.

As to why the maybes, consider the following model:

^{simulate this circuit – Schematic created using CircuitLab}

If the thermal resistance from the die to the heatsink is much larger than the thermal resistance of the heatsink to ambient, and the thermal capacity of the die is much less than the capacity of the heat sink (and I would guess both to be true), the latter is the dominant factor in determining the thermal time constant of the heatsink, and thus of the die. In this case, increases in the die/HS thermal resistance will have only small effects on the time constant of the die, but will cause the die to get hotter. You'll have to figure the values for your board to see if this is the case.

I think you could do this. Suggest serpentine tracks that don't form a coil so that the magnetic field won't be especially strong. You can shield electrostatically with a ground plane, but the magnetic field will go right through everything, so if you have sensitive circuits you might need to filter the PWM to something more like DC (not really a big deal, just some inductors and capacitors).

The copper thickness and resistivity and etching of fine traces are not that well controlled, but +/-20% is not a big deal on a heater (and you might be able to get that repeatably).

Personally, I'd use a cheap SMT thermistor for the sensor assuming you only want to control at one temperature. Just stick it in and it will work. There will be excitement enough getting the heater to work well.

Here is an example of a pattern used in a commercial film heater:

Yours would have to jog around through-holes, but if you splurged on blind vias that could be minimized.