Its more about the thickness of the layer of substrate in which you are using on the bottom of the cage, certainly if you are using a UTH like flexwatt.

Basically, a thick layer of substrate would serve more as insulation against the heat rather than conducting it through to the rest of the cage.

If your cage temps aren't where you want them to be, use less substrate on the floor. Another dimension to this is that the more substrate you use, the less you tend to completely change it out. Using a thin layer will boost your temps as well as make it easier to see when the cage needs to be cleaned. You'd be suprised how much urine can build up at the bottom of a layer of repti-bark or aspen shavings....