I can see how you could get confused. The jurisdiction of the EP over the New Territories is defined by a Patriarchial Synodal act from 1928 and that jurisdiction, while canonically significant, is practically much less so. The areas included are parts of Epirus, Macedonia, Western Thrace and northern and eastern Aegean islands. Here’s a link to a new study of that act and its effect on the ground done by the Phanar recently:
http://www.ec-patr.org/docdisplay.php?lang=en&id=790&tla=en
You are correct that half the metropolitans in the synod of the Church of Greece are from those territories, but the synod is made up only of the metropolitans of the 12 metropolises of modern Greece. There are over 100 dioceses, as I remember it, and at least 75 of them, where most of the people are, are under metropolitans of the Church of Greece.
You may remember that there was a mini schism a few years back when Athens appeared to violate the 1928 act.
As I said, I was under the impression that only those areas of Greece that were part of the Greek State of 1830 were included in the jursidction of the Church of Greece (established in 1833, and recognized by the Patriarchate in 1850).
This also made sense when it came to the makeup of the Greek Synod, namely that 50% of the bishops are from the Patriarchate.