Solder mask resist on extra large through hole pads
Yes you can do that.  Often for smaller pads the expand the soldermask to allow for PCB fabrication tolerances and prevent overlapping the pad with soldermask, which of course will prevent solder from reaching the pad.  But for large pads, there's nothing really wrong with keeping the soldermask solder if you don't need to (or want to) allow solder on the entire area.

The good thing about doing it is to keep the board looking cleaner.  You can also use the area to apply silkscreen if you want.

But, in your case as you are doing this for thermal management, leaving the copper exposed may be preferable.  To Tut's comment, yes certainly soldermask will impede heat dissipation somewhat, but not too much, e.g. as compared to dissipation from an inner layer which has thicker core material covering it.  What the soldermask prevents though is applying more solder to the copper to increase the copper volume which will greatly improve heat dissipation.