Hourglass and libTAS are not emulators, so they don't emulate the hardware. They intercept the game workflow and control it. Since they only work with applications, their movies start when the applications start. It's impossible to include anything else.
JPC-RR and all the rest are emulators, so the movies start as soon as the hardware is turned on along with software we're running on it. There's no easy and obvious way to say "the game launches
right here" about any moment in time.
For those curious, no one forbids posting movie time calculated from game startup, but the movie system (and therefore, submission system) have never been designed to account for the difference between bootup time and actual game startup time.
I'll see if the rule wording is outdated.
EDIT:
I think there's no ambiguity in the actual rule talking about starting point in the general sense:
http://tasvideos.org/MovieRules.html#MovieMustPlayTheGameFromTheBeginning