1) No, it does not really send a GCode. But it has the same effect as sending M220 Sxxx. Yes, it effects the minimal layer time. And it effects everything.
2) "Sleep..." indicates an error. It's a bit of a bug, as it should say "ERROR: TEMPERATURE". Most likely the thermocouple connection is a bit bad which is causing this during certain movements.
3) Long filenames are currently only supported in the unstable development version of Marlin.
4) The issue here is that we don't know why you pressed stop. You could be pressing stop because the hotend dug itself into the print, at which point you DON'T want it to move. You could also have pressed stop because the print failed, and you want to restart it. Cooling off the nozzle would also be bad then.
5) Yes, the menus are a bit overkill at the moment. They where designed when a lot of settings where not dialed in correctly yet. Now they are and you no longer would need those menus.