Yup, I contacted Dion from Spyder Robotics, and he said he was sure using different lengths of Flexwatt would result in different temperature ratings from each run.

"They will not all be the same temp. There are differences in heat output
between different lengths of flexwatt and often even in the same lengths of
flexwatt even when they are at the same voltage. Its not an issue with the
thermostat but the difference in resistance and environment of the heat
tape. Even with a simple rack setup where every level has the same length
of flexwatt the top racks will be much warmer than the lower ones due to
heat naturally rising. However, in a standard rack its usually a couple of
degrees difference top to bottom which is not enough to cause a concern.

So typically when building a rack you want to keep the enclosure size the
same throughout the rack so that its easier to regulate."

Dion Brewington
Owner, Spyder Robotics