Can you specify a separate current limit for both the Heating and Cooling modes in the 54100 series TEC controller?

Yes. We can set Positive Current Limit for Cooling and Negative Current Limit for Heating separately. For example, we can set +3.5A as Positive Current Limit for Cooling and -2.7A as Negative Current Limit for Heating. Traditionally, TEC is for Cooling in most cases. So the polarity of current for Cooling is defined as Positive.