Well, I'm not sure, but I think some things are left behind because there is certain data and stuff that is generally usable by other programs, so it isn't removed when the program is. Back to the other subject: I wouldn't even worry about the eMMC unless you start having serious problems and can't find another solution other than reflashing back to the stone age, so to speak. When you feel ambitious, learn to run Ubuntu from a CD. It's fun, and it would make flashing easier for you when you need it.