I think you're making it more complicated than it needs to be. Ideally, the WAP would be always-on. Or perhaps your switch would control its power directly.

Why do you want the WAP to shut off when the empeg goes into standby mode? The whole idea is so that the empeg can sit in standby mode waiting to be synchronized.

(You do realize, that when you check the box "power off empeg when complete" in emplode, it doesn't really mean power off, right? It means go into standby mode.)