If investee companies have already set SBTs, can this be counted towards reaching an FI's portfolio coverage target or do new investees need to set SBTs?

That is exactly what the Portfolio Coverage method does. You measure the proportion of your portfolio that has set SBTs and then set a target that makes sure that 100% of your portfolio has set SBTs by 2040. You find more about this method on p 80 of our guidance.