i did a run for any percent console which in the end the time was sub 53 however when it was verified it was sub 56 . So how does the timer work?

Firstly, your IGT was a 53, not a sub 53. And your run was verified as a 56, not a sub 56.

Timing begins on difficulty or file select (if no difficulties unlocked) and ends on the fade to black after beating the game.

in game time is inaccurate. for console runs, they are timed real time. this includes all pausing and load time

oh ok