Regarding display index:

Output 1 and 2 default to display-index 1
You need to change output 2 to display-index 2 (as you discovered)
Output 3-6 are actually fixed to display-index 3-6 respectively, despite whatever you select on the dropdown menu

Also note that the sequence in which you connect the displays will affect the display index.
It is not necessarily logical!…
Changing the screen layout order to match catalyst, in system preferences, can help some confusion
Essentially - the OS decides what it wants to do - best option is to accept it and move your LCD or use a matrix to acquire your desired layout

S