The reasons for the separate downloads are twofold:
1) Ease of updating. The graphics files are not likely to change, but the missions and tables are pretty fluid, due to bugfixes and so forth. With the separate files, we need only upload small fixes instead of a huge file.
2) Ease of downloading. The only required file is the root VP; all the others are extra. People with slow connections can download the small file with the required stuff and aren't forced to download megabytes of data they don't need.
If we had a utility to extract all the FS1 data files (cbanis, sounds, voice, etc.) that would be pretty handy. I'd prefer not to have an installer, though.