I have gone back and forth with that so many times. Most GA airplanes I flew had the Audio Panel at the top so there's that. All the airplanes I flew with the AP panel at the top had autothrottles, so there's that. I reasoned that many of the functions on the AP panel required a power adjustment, so why not put it close.
Audio panel on top? There are historical reasons for that and those reasons no longer apply. Back in the bad old days of tube radios, before there were flip-flop radios, a pilot would listen on one radio and then tune the other to the next frequency. Then to switch radios, it was go to the audio panel, turn off the old radio audio, turn on the new radio audio, and switch transmitters.
With flip-flop radios, you don't have to do that. Once things are set, you hardly need an audio panel. In fact, you hardly need two radios any more if the comm radio can monitor a standby frequency. I've flown single comm radio for six years now and never looked back.
The second reason that audio panels were installed atop the panel is that often the cowling sloped down ahead of the windshield, and old style audio panels tapered down at the forward end to match the limited space.
As for putting the autopilot panel next to the power knob because they get used at the same time... Maybe sometimes, but not all the time. When you move your eyes over to the autopilot panel so you can push the right button, it's easier if you don't have to move your eyes down.
As for your choice of GPS, I think there's a better option. The GTN650 (or other GTN6XX) has more screen real estate, and that will be handy when you are editing flight plans or fussing with approaches. Plus, if the GTNxxx has a comm radio built in, those frequencies will be displayed all the time and the knob will default to them, so in terms of usable GTN screen real estate, a separate comm radio costs you and provides no benefit. And if you've got another comm radio already, you're covered.
I'm not sure how things get wired up if you have the VHF NAV in a separate box, but with the VHF NAV in the same GTN box, the system will automatically transfer from GPS guidance to ILS guidance... if you set everything up correctly.
What would I do if it was my plane? Autopilot on top; GTN750 underneath to get effectively one more MFD screen; Comm 2 or Transponder underneath; and audio panel under the right side screen, 'cuz it will almost never get used, once the intercomm is set properly.
You said that you go back and forth. True confession, so do I, sometimes...