Substrate serves three purposes:

First and foremost....it is there to absorb wastes.
Second....sometimes it is used to enhance the appearance of an enclosure (make it look more natural or fulfill some other "design" choice)
Third....occasionally, an animal will want/need substrate for its comfort, either to burrow in (most common) or for cushioning its floor.

Ball Pythons don't need it for comfort. They only need it to absorb wastes. Whether or not you want it to enhance the appearance of your enclosure is entirely up to you. If you don't care about that....simple paper towels or newspaper will suffice. If you want it to "look nice"....repti bark is fine...but you only need just enough to cover the floor of the enclosure. You don't need to build up a "thickness"....and as you've already seen, having a deep layer causes complications.

Jamie is right that you want to be measuring the temps at the floor of the enclosure rather than on top of the substrate....a thin layer, just enough to cover the floor....makes this much easier to balance out.