You don't want the water bowl covering the entire UTH, because that would mean your snake can't get to the hot spot (unless it can get under the water bowl). However, having the water bowl on the UTH is a good way to raise humidity and there is nothing wrong with it.
I am confused how you have a mesh top on a sterile enclosure?
Also, the cardboard hide you mentioned should only be used short term until you can get a better one. The cardboard could be a breeding ground for germs just as much as the towel could, and you have no way to disinfect the cardboard.
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