They would be more vulnerable to any extreme of temperature
Let's look at two 1 kg dry bags of flour with an internal temperature of 37°C sitting on the floor in a room at 37C and minimal humidity. Now pour out Bag 1 and blow it around with a fan. The individual particles of Bag 1 will still have a temperature of 37°C. Bag 2 will also retain its temperature of 37°C.
Now take two new bags of flour, still with an internal temperature of 37°C, into a room at 20°C and repeat the experiment. The individual particles from Bag 1 will very quickly approach 20°C, while Bag 2 will be much slower to reach 20°C. It would be a matter of seconds I would think before the temperature would drop to below hypothermia levels.
Repeat the scenario again in a room at 45°C and the Bag 1 particles will heat up faster, while Bag 2 will take longer to heat up. As observed in the question, increased surface area will change temperature faster through conduction and radiation (convection is a bit iffy with the small particles), although see point 3 below.
However, there are three additional factors:
- Evaporation - without some special mechanism to maintain the integrity of the particles the water in the superhero's body will evaporate away very quickly, resulting in the superhero reconstituting as a mummy. (Which could be a really scary, albeit fatal, ability to intimidate the bad guys with.) If the thought experiments above were repeated with wet bags of flour, the particles from Bag 1 in the 37°C scenario would cool instead of retaining their temperature and the particles from Bag 1 in the 20°C scenario would cool much faster.
- Heat generation - a bag of flour is not a good approximation because human bodies are generating heat all the time. Maintaining a levitation field to keep all the particles together may mean even more heat generation, which could offset the heat losses from conduction and radiation. However, if this is the case then it exacerbates the evaporation issue and the risk of hyperthermia in environments over 37°C.
- Non-interaction with other particles - if the molecules of the superhero's body avoid interaction with other molecules in order to pass through solid objects (implied by "separate the molecules of other materials" in the question) then convection and conduction are by implication not a factor and radiation is the only mechanism for heat transfer. This makes the calculation of heat loss quite different, as it would require calculating the black body radiation of each of the molecules of the superhero's body and summing these. However, if the levitation field is keeping all of the molecules close together (keeping the molecules as close together as if they were a solid) then many of these molecules will be radiating to each other, which makes the net radiation of the entire body approximate to the black body radiation of a normal human body. This raises the issue that if the molecules all remain very close to each other and do not lose heat through convection or conduction then the risk changes from hypothermia to hyperthermia - the human body needs to be able to dump some heat to its surroundings through conduction and/or convection in order to avoid overheating.
In short, heat loss is a factor that you can use to put limits on how long your superhero can remain in "dust" form without suffering hypothermia, but you need to ensure that the explanation of this power prevents death through dehydration as part of the process.