Are thermal effects on an FPGA different depending on how it is programmed/configured?
Sorry, but both a microcontroller and an FPGA will have different thermal behavior depending on how they are used. If you intend to do thermal cycling or life testing you must run the application software (or similar) on a microcontroller and apply the application configuration (or similar) to an FPGA.
You need to be careful to differentiate between the thermal properties (which depend only on the physical construction and packaging) and the thermal behavior (which depends on usage as well). For thermal cycling and life test you want to be sure that the die itself is as hot, and in the same places, as it will be in use.
EDIT: It sounds like your real problem is that you haven't convinced the customer that your &quot;TCS&quot; really is an overstress. If the customer remains skeptical then you have no choice but to run the actual application software. If you are trying to demonstrate something about reliability or failure rate, then running a test without application code (or demonstrably worse) is no test at all.