That would be correct, because "Configuration Settings" is the description given to files with an extension of ".ini" at the end of them.
Abosolutely.
If you would like to explicitly see the file extension for your filenames, you can "
Show File Extensions in Windows 7."
That behaviour is not weird because it is the expected behaviour. You must start up the game version (and perhaps start a new game or load an existing game, then play through a turn) before certain files are automatically created for you. Start up BTS, play a quick game for a couple of turns, then exit BTS. The relevant CivilizationIV.ini file should have been created for you.
Beats me how lines could be missing, but again, I'd say start up Vanilla, play a couple of turns in a game, then exit Vanilla. Doing so should hopefully correct any missing lines in your CivilizationIV.ini file.
My CivilizationIV.ini for Vanilla is found at this location: \My Documents\My Games\CIV4\CivilizationIV.ini. There are definitely two lines in there that say:
; Specify a Mod folder (Mods\Mesopotamia), '0' for none
Mod = 0