I'll try and answer what I can here:
#2 - there is currently no way to stop LB regenerating the folders as far as I am aware.
#3 - Yes, once Big Box has loaded in the background you can stop an intro video by pressing the "Accept" button on your controller or Enter on your keyboard
#3.1 - Yes, create a folder in you LB folder called Startup and place your intro videos there, it will choose them randomly on startup.
#3.2 - yes, go into the Sounds folder and either delete the startup sound or change the filename, then it will not play on startup.
#5 - if these games are already in your arcade platform you can simply delete the Daphne playlist (or any arcade playlist) if you wish