In 1.0+, hidng parts in fairings are availalbe in the stock game... At least this workaround still works... (I haven't tried it on a probe core inside a service module inside a fairing, which also seems possible now...) (I have a multi-payload vehicle in a fairing and it took one of the sub-vehicle's pod as the control point, with the probe core that is intended for the first few stages hidden away...) A nice way to do it would be to allow the "control from here" for the VAB or SPH, preferably with some indication on each possible control point whether it is default or not... (Having priorities might be useful for a vehicle with sub-vehicles) (Although adding it as an option in action groups will also help..)