The engine controller is separate from the tcm. Simply flash a tcm with a 80e flash and run the CAN lines and trans wires. The trailblazer OS has nothing to do with it working. That's the engine side.
We've done a few a few LS3 engine harnesses with the 80e behind it. It'll work.
I need to know the specifics on what u have but it sounds like it shouldn't be a problem.
PM me or ray.