Thomas,
Aside from the software, a physical % measure of an entire project would be difficult to determine. When considering a single aspect of work, eg, metres of piping, or cubic volume of spoil, you have a very tangible measure of physical progress. But what if your project consisted of both piping and spoil?
In those cases you need a common denominator for measuring the effort. This is the method that Earned Value adopts, but using common denominators of Manhours of work, or cost in Dollars, as these can be equally applied to both type of work and then aggregated to give overall project % complete.
The above is one reason why when using physical % complete in P6, it wont aggregate at a group level.