There is an option with some defrag utilites to select boot time directory
consolidation, which moves all the directories together at the beginning of
the disk partition, instead of leaving them scattered throughout the disk
(based on when they were created).

I read that doing so is beneficial, especially for FAT32 volumes (presumably
in terms of access times to get to the folders and files).

My current setup is this:
C: system and boot up (the main partition). NTFS (60GB)
D: FAT32 partition for misc files (40 GB)
E: FAT32 partition for music files (40 GB)
F: FAT32 partition for video files (80 GB)

My question is this. I did that on my D: FAT32 partition (C: is the NTFS
system partition). Is all the information on where the directories and
files are stored on D: contained on the D: partition, or is it also stored
in the root C: partition in its MFT?

If the actual location of the directories on D: is stored on C: in its MFT,
or whatever, I can see a potential problem if both C and D are not both
archived properly in terms of making backup images (in case one needs to be
restored and is unaware of the changes in the updated directory locations)

I presume some of the information on the directories location is contained
in C: too, since otherwise it seems to me you would NOT need to use a "boot
time" directory consolidation option for the D: partition, but could instead
do it live (with Windows running).