How can I disable XQuartz entirely and use Xorg with my own Desktop Environment? I want to use i3, which is available in Mac Ports. I've installed it and xorg (with ports install xorg). Now I want to boot into that. I've tried created an ~/.xinitrc and an ~/.xinitrc.d/99_i3 script (both had +x). But in neither occasion did X start up with the script. Is it possible to use Xorg on boot and jump into i3 instead of the normal OSX Window Manager?

You can find a very similar question on SuperUser here.

Just to be clear, I don't want any OSX functionality. I'm only not reformatting and installing GNU Linux because my company prohibits it. I want to bootstrap a parallel configuration with ports and boot into an i3 environment (ideally with no dock, Aqua, Finder).
If I have understood you correctly, what you actually want to do is to get rid of the Mac graphic environment, and run a "classic" X11 session instead. Correct?

I don't think you can get rid of the Mac graphic environment entirely (short of installing some other OS, like *BSD or Linux), but you can hide it to a certain extent.

Configure Xquartz to run in full-screen mode (it's in the settings somewhere...). This means you won't see any Mac stuff. Create an ~/.xinitrc file. Xquartz will run that file on start-up, just as would normally happen with startx or xinit. In that file, you can start any window manager you like. e.g. good old twm. (If you don't have an .xinitrc file, Quartz will start the quartz-wm window manager, which gives a "Mac look" to your X windows.) It should be theoretically possible to get an entire Gnome desktop running, but I have not tried that... You'll still have to boot into MacOS and log in to a Mac desktop, but after you have started Xquartz, you should be back in familiar X11 land.

(I get the impression that you believe Xquartz is the standard graphic Mac environment. It isn't. Xquartz is an X server that runs on top of the Mac graphic environment. I think Xquartz is just a packaging of the Xorg server, built for macOS, but I could be wrong on that.)