Hello to anyone still following this long thread.
I attempted an install of notepad++ version 7.6.6, using the 64 bit installer, as both a normal user and an admin user. I took full debug logs from both, which are attached.
Because they are full logs, I have marked them as follows:
A single star (*) above any error, warning, or group of same.
Double stars (**) at the start of the section which shows when I first launched the installer.
A star dash star (*-*) above the main string of errors in the normal user log, relating to the window with the missing tree of checkboxes.
I hope this helps someone figure out what's going on here, but it seems to me that a lot of information that should be included in NVDA debugging, isn't, so I am not hopeful.