- The CUE maps the audio in a "CD-native" way, like each track can have 1 or more indices, which enables things like pregaps. When you split FLACs into discrete tracks you need to figure out how to project that onto files, do you put the pregaps at the end of previous tracks? At the beginning of next tracks? In short, with a CUE you can emulate the CD experience more accurately.

- If you are seeding a torrent, you need to keep the original data intact.