Oooh I see now. comparing 2 runs side by side is pretty clear. The transition happens earlier if you don't pause.

Ah fair enough, how comes it doesn't save time? does the timer still run on pause?

So not sure if this is known or not but when you get to the gate near the start of Y Island, if you start the gate opening animation and pause the game the animation will continue during the pause menu. Unpause when the animation has finished to save a few seconds. 

I've not fully tested this with times but I'm assuming game time is actually paused during the paused screen.