If you're using Windows, no, that's inherently the clumsiness I was describing. If you're using Mac, I'd say, yeah, kinda. The thumb can easily and ergonomically handle the space, cmd, and option keys.
IMO, all your examples fall under the awkwardnesses that I had mentioned. Under a normal QWERTY layout, ~, 1, Tab, Q, Caplocks, Shift, and Ctrl are all controlled by the pinky. Under Windows, executing a simple CTRL combo means the pinky is no longer responsible for ~, 1, Tab, Q, Caplocks, Shift. That all moves to the ring finger, as you said, which means you've moved away from the normal home row typing position. Quite clumsy IMO.
Vs Mac, the thumb uses CMD, and the pinky remains in home row typing position and can handle all the keys it was originally responsible for. Both hands can stay on the home row at all times. Many simple keyboard combos can now be done with one hand without "exception logic" that runs contrary to standard typing. ctrl+shift in your example becomes cmd+shift, all easily doable on one hand. This also unlocks lots of mouse + keyboard combos since many left-side combos can now be done easily with one hand.
For the skilled typist who is very familiar with touch typing, more complex combos using both hands are even simpler now, because both hands can stay on the home row.
> If I use left-thumb for left-command instead then I can only figure a way that involves moving that hand completely away from the home row
I'm a little puzzled by this, why would your hand have to move away from the home row? Just so we're on the same page, on a Mac-standard keyboard, the cmd key is where the alt key is on a Windows-style keyboard, so directly adjacent to the spacebar.