Personally, I think it's the stretching a finger in the direction it's pointed towards vs. bending a finger that crosses under other fingers. I find the first to feel much more natural. Although I've been a Mac user for years now and have gotten used to the cmd key, ergonomically, I think ctrl makes more sense.
I definitely agree about the ergonomics. When I first switched over to mac, it was so hard to adjust to the position of command key, especially for copy and pasting. For windows, I was able to copy and paste without moving my entire left hand down. Meanwhile for the command key, I have to move my hand downwards to reach the key. Although it's not that big of a movement, it definitely took me some time to adjust.
I'm a fan of the pomodoro method, although always found 25 minute cycle to be too short to actually concentrate. Personally like the 40 minute - 10 minute cycle more.