I'm using a very custom keyboard configuration and I'm doing all my config using Linux's xkb (X Keyboard Extension).
I'm for example using "modifier + ijkl" to send actual arrow key codes so I don't need to move to the arrows key cluster. It's not unlike gamers using wasd or esdf: ijkl mimics the arrows keys cluster. It just "makes sense". The modifier is always under my left thumb (I'm using a japanese keyboard, so the space bar is very narrow and I'm using the key at the left of the spacebar as the modifier for ijkl (and for other shortcuts). This is sweet because as actual arrows key code are sent, this works in every single program as if the arrow keys were actually pressed. I'm sure it can be even better: say by doing it at the keyboard controller level, bypassing the OS entirely but what I have works well enough for me.
Another trick: a modifier dedicated only to my window manager. Anything I need to do that is related to the WM gets done using a dedicated modifier. Never clashes with any single program. Bliss.
I do other cute things: OP mentioned using Emacs a lot... I configured things I use in Emacs all the time, like ivy / avy, to never require the pinkies (I removed the keys supposed to be pressed by pinkies from the list of available candidates).
Stuff like that. I spend countless hours on my keyboard setup and, to me, it's perfect. I did that years ago and since then I'm a happy camper.
> And then my mind has blown up.
Then I have one for you: you can use something else than ctrl to do ctrl-x in Emacs, using ctl-x-map. I'm using "key at the left of my tiny space bar + ." to do what ctrl-x does. No pinky and both hands are used (instead of doing left hand for ctrl and left hand for x).
> No more weird thumb positions, or elongated pinkies.
I don't really understand how you can get weird thumb positions on an ergodox though...