A mod on an AT vs. a MT car will make the same power either way. It's the difference in parasitic driveline losses incurred by each transmission type that will affect final power output at the wheels on a dyno.
I am not familiar with the specific AT/MT parasitic driveline losses on the Z, but I'm sure if you do some research on dyno numbers of stock AT vs. stock MT, you might have your answer, but each dyno is different so it's hard to say.
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