Raw PWM is one of the worst and lowest efficiency methods of controlling a TEC. Filtered PWM giving low ripple (i.e. effectively a buck regulator) is fine.
Really? ok, i probably should look into TECs a bit more.
The point is simply this: resistive losses are I^2*R. Running the TEC at 100% rated voltage and current you get the rated efficiency. Now if you run it at 50% duty cycle but still 100% rated voltage and 100% rated current (during ON state), you are still running at rated efficiency; not any better, not any worse. But if you instead run it continuously with lower voltage, you get better than rated efficiency. Same thing with LEDs. Efficiency goes down as current goes up.
On the other hand, if you have designed your Peltier gadget (specifically hot side cooling, which is non-trivial to get right) to work at 100% duty in some conditions, and can handle the heat it generates at that point, then surely PWMing to lower power will not be a problem: you have less heat to work with. It's only that by PWMing, you miss the opportunity to do
even better, but if the design handles full power, then one could question, why bother optimize the partial-power use case, especially if it's a scientific instrument (or a toy, for that matter) where energy cost is not that important.
(And if energy cost is important, you would not use a Peltier at all.)