A more detailed information could be helpful.
3) Your first drawing shows: "turn ON Y" then, without any other code it goes to "turn OFF Y".
--> With the speed of a microcontroller there is a good chance that Y never really gets acivated.
4) Your interrupt solution:
Let's say timer periodically fires an interrupt. Within this ISR it just "turns ON Y". After that immediately it returns to the MAIN loop, where it "turns OFF Y"
--> Maybe this is right, maybe wrong, we don't know. We have no information when you want to switch OFF Y.
5) you say "it's faster than method 1".
The microcontroller will work in low microseconds, but X and Y reaction time is in the milliseconds range. Thus I see not much speed benefit.