Hey there! Welcome to the Mac Car forums!
Interesting that you are using the mac as a media server with no monitor and such. As far as powering on/off the mac with the carnetix PSU, I have personally never tried that. I use momentary switches/buttons, one to control the regulator, the other to power on/off the mini. When I want it off, I would press (and hold) the power button until my mini shuts off. Perhaps the same philosophy might work in your situation.
Thinking about it some more, you can setup your mac (before removing monitor and keyboard) to bypass the welcome screen and go straight to the finder (or open an app at startup) through control panel. Now if you use the mini's power button, you would press and hold it until the mini turns off. Another alternative might be to wait for the regulator to power off, and 30 seconds to a minute later, the mini turns off as well. But to use the PSU to turn it off, if there's a way to create the same pause effect that occurs when pressing & holding the mini's power button, then that may work for you.
Sorry for the rambling. I'm in the midst of rewiring. I hope some of it helps you. If I do stumble on a better answer, you'll hear from me...