Usually for home theater setting. Some people just can't be bothered to switch it for stereo and leave it as is. Some receivers has a function that do direct and bypass the digital part but based on my finding on my Pioneer 43Tx I still have my sub going even in 2 stereo direct mode unless I have set it up wrong. Anybody try out direct mode analog and see if your sub stop working?
Personally I just run my mains for 2 stereo ... I have a passive pre-amp that let me do it and switch inputs. Its really a matter of preference for each individual. Whatever makes you happy to enjoy your music is the most important.