index.bin is something different; it stores information about resources created through the extended editor and is responsible for their display when the editor is restarted. The default index.bin also handles the display of developer objects in the editor, and the NCF version, I think, handles the display of new creatures in the tab that allows you to place them on the map through the editor. The NCF core itself is an executable file in which the constant responsible for the number of creatures in the game has been changed (by default, this is 180, increased to 1000) + the Creatures.xdb file has been modified.
The main thing is in the .exe file, because even if you write anything outside the .exe, the game will give an error and nothing more!
Yes, as far as I understand, you are all correct.