but with the thumb on command, you have to contort your fingers to hit any of the alphabet keys.

On a Mac keyboard, you have two Command and Option keys. That means you can combine your (left|right) thumb on the Command key and a (left|right) finger on another <key>. Moreover, you can naturally use Ctrl-<keys> as a Control-Character in a Terminal. Which is sometimes a pain on Windows.

Try Cmd-w (close), Cmd-X (Cut), Cmd-C (Copy), Cmd-V (Paste), Cmd-Z (Undo), Cmd-A (Select All), Cmd-Q (Quit) with your left thumb on Command and the left index on the other key. Try Cmd-P (Print), Cmd-, (Preferences) with your left thumb and a right finger. I'm using macOS and Windows since the 80s, Gnome and KDE later; I still think that Windows and Linux are generations away from macOS consistency and ergonomic...

Moreover: on macOS Cmd[-Option][-Shift][-Ctrl]-<key> is always about a menu item/command shortcut; [Option][-Shift][-Ctrl]-<key> is always about a glyph.

well [ctrl] + <down arrow, F4, F5> are used for window management by default

I agree you still have to contort your hand but it is significantly less movement than using your pinky.

IMO you should remap your keys: https://karabiner-elements.pqrs.org/

Every system will not be 100% to your liking, so make it work for you.

So, I don't remap keys anywhere. This is because I move between Linux, Windows, and Mac OS on both laptop and desktop and multiple external keyboards connected to montiors. No mapping actually obtains a sane behavior that is consistent across all platforms, terminal applications, and others. I've tried and it always ends up messing one of M- (meta key prefix) or control keys.

I immediately had to get Karibiner to at least give me my home and end keys back on a external keyboard.

I've been to aggressively remapping that I don't then create a similar problem when using another machine I don't own but maybe I'll give in and go the more custom route