I've done a little research on what the new 'Natural Arrangement' option does to MST harmonies, using the notation function.

Two findings so far: First, MSTs are considerably affected by the NA option. Second: NA can radically alter the harmony.

I've tested alts, because of the number of alterations (b9, #9, b5, #5).

The piano MSTs I've tested use #9 & #5 for alts. I've not found b9 or b5 included so far.

With NA enabled, lots of 9ths & 13ths suddenly appear - a very different harmony.

Interested to hear if any other nerdish types are looking into this.

Best - Andy