The online knowledge base is a little better than the manual.
But here’s the gist of it:
The idea was that Windows users would use Windows Media Player/Sansa the way Mac users use iTunes/doPi. So Auto Detect defaults to MTP mode, controlled by Windows Media Player, if it detects WMP 10 or above. WMP is supposed to refresh in the background so you don’t get the long refresh times.
Subscription services like Rhapsody and some Audiobook software also like MTP because it can send over hidden lock/unlock codes.
Unfortunately, WMP is not as smooth as iTunes with Apple players, because Apple only has to work with its own gear and can test every piece of hardware. (And iTunes is a crazy resource hog, and tyrannical, and ugly, but don’t get me started.) Windows has to work with everyone else, inviting more variations and errors.
Meanwhile, lots of people prefer direct control, offered by MSC (which also lets Apple and Linux users connect to Sansas), which sees the Sansa as two basic flash drives.
It was good of SanDisk to offer the alternatives. Some players are MTP only, which is just ugly. But SanDisk could explain better, and the mode switch can be a real mess.