Honestly would rather it skips the SP3 but still passes the timer by the SP3 length just so it doesn't get annoying to have to use SP3's, or make the timer pass by a set amount to compensate for different SP3 lengths
Timed meaning AQ, AW, Battlegrounds and Incursions
That would be a nightmare to program so it could subtract the time of the Special, and then synchronize for Alliance Events.