adding second note to existing one: difference in retaining correct octave

The 1.3 approach is more natural "sometimes" - it depends on what you are doing. you have clearly entered the top note first and want to enter another below, but MuseScore has no way of knowing this. And in fact, in 1.3, it ends up guessing - some notes get added above, others below. So it's harder to predict, and more importantly, even when you can predict it, less efficient. The 2.0 approach is optimum *if* you always build your chords bottom up. If you do this, you never need to use Ctrl+Up/Down within a chord except for notes more than octave apart. Once you wrap your brain around this, it becomes very efficient.

if you prefer to enter chords top down, the efficient way to do that would be to use Shift+number rather than Shift+letter. And the nice thing about doing this for things like adding a harmony part a third or sixth below the melody is, you don't even have to think too hard about what note you are adding. Shift+6 over and over will always add the harmony a sixth below. You can even just select the whole passage and pressing Shift+6 to enter the harmony part in one go.