The point is:
LEMD TORA
36R 3500m
36R Y1 = 3500m
36R Y2 = 3445m
The threshold 36R is definitely past Y2
http://www.aena.es/csee/Satellite?bl...&ssbinary=true
so I don't think you'd be loosing 45m lining up from Y2
Conclusion you are expected to start your takeoff roll from prior crossing the THD?