So to summarize your use case: you needed T-PROT removal on EDC17C60 because PCMFlash 1.20 wasn't bypassing it during OBD read/write, and this tool got the job done. Now with PCMFlash 1.21 the T-PROT bypass is handled natively, making this tool unnecessary for that ECU — at least via OBD with PCMFlash.
Still potentially useful for anyone who:
Is stuck on an older PCMFlash version
Uses a different read/write tool that doesn't handle T-PROT bypass (e.g., some KTag/Autotuner scenarios)
Needs to patch a bench dump where the tool's OBD bypass doesn't apply
Did you get a chance to test the MD1CS003 side of the tool as well, or only EDC17C60?