So if the speed boost doesn't active for 4 seconds after the yellow line and your timer is supposed to start right after you gain the speed boost does that mean those 4 seconds don't count?

actually I thought the same as you and counted the run from the speed boost but I guess it also starts from when you touched the yellow line

I think so since getting that long of a boost isn't usually common at all and would be an unfair advantage towards the other runners.