why does the timer start as soon as we press reset instead of it starting as soon as you select a file?

I guess that was the way it was traditionally, so they kept it like that

Was it used in Japanese runs?

Its an older timing method than file select, but not super uncommon. There's a lot of different timing methods, like SDA timing which starts on first input, or TAS timing which ends on last input

japanese players in 2009 decided on it

not as bad as alex penev's stop timer on the cake picture at least