Separate-Ground voltage measurement

Both circuits should work just fine - build it on a breadboard and try it out with two Pro Minis. Your circuit is indeed a bit simpler, and if power is not a concern, go for it (battery power usually means it is a concern).

The value of the resistor in for the opto is indeed not critical, especially in this case as you only need small signals. 1k3 will work, 2k2 may even still work. Whatever you have on hand.

To program a tiny (for the future maybe), you can use an Arduino as ISP. That's my current method for programming them.