I see two different types of complex encounters here:
1) Encounters where it makes sense there would be reinforcements: Attacking the gate, guards outside the guards' barracks, etc. My suggestion is to factor the reinforcements into the encounter - but then there is the question of what effect the delayed entry of a foe has on an encounter. Attacking 12 goblins is different from attacking 4 goblins with one more goblin showing up for the next 8 turns, even though both are the same XP. I don't know - scale the XP of foes that are delayed in showing up? Or just ignore it - like a bit of terrain that automatically favors the PCs?
2) Adventures where the point is to sneak past the roving guards because if you don't, something bad will happen. In this case, I think the best call is to figure out what the "something bad" will be, and create that encounter. Then consider that encounter to be an event driven encounter - when they are noticed, this encounter occurs. If you want, you can then figure out separate encounters with parts of the event encounter: these 4 goblins are in the barracks until the alarm sounds - if you fight them in there, and kill them without sounding the alarm, then they won't be in the big event encounter.
Does that make sense? I'm not sure how well that will actually work for adventure design - I'm worried that the XP scaling will make it hard to split up a large encounter into smaller encounters and still have it challenging.