Looks a bit like you're on your own in this Emacs community @rglullis@communick.news - Howdy!
The ediff-split-window-function and ediff-window-setup-function settings should really be the defaults. I think I set them back in the 90s, and I didn't realize ediff was so new then. But I bet the vertical split default was because back then a lot of people had 1024x768 fuzzy CRT monitors, but that floating control frame was always awkward and annoying to me. I was so stoked back then to get 1280x1024 and comfortably have two windows side-by-side.
I've been happy enough without any more customization. Most of the time I use ediff through magit and then it's all pretty smooth and easy. I hit e on a diff or conflict and it pops up, and when I quit it my windows seem to restore logically. I have to admit I didn't digest the elisp etc, later in the post. I wasn't that motivated since I don't seem to hit the pain points that this was solving.