I would pull the wires from the two speaker pairs to the location for your receiver (or what ever may replace it later), and choose hook up options after construction. If your father is truly preparing for Dolby 7.1, a new processor and amp will be required for the additional discrete channels.
In Dolby 7.1, the rear speakers are configured very near one another in the center of the rear wall. Playing Dolby 5.1 from these center rears will not help his current system, and may provide too low an impedance for his current amp. Even if the switch box provided his amp with a safe load, the time delays and speaker position will be wrong for his current Dolby processor (as you stated).
The switch box will be not only provide an insertion loss, but also an unnecessary expense along the path toward Dolby 7.1. Waiting until the construction is complete may put him in a position to be able to choose from any number of new Dolby products that will resolve these issues. It's great that you're helping him avoid this unnecessary and possibly damaging expense.