only native French people with ancestry going back to the Ile-de-France region for at least a few generations were taken into account for Haplogroup

No, only native French people with ancestry going back to the Ile-de-France region for at least a few generations were taken into account for the studies. There are two possible explanations as to why the Ile-de-France has more E1b1b and J1:

1) The region was more heavily settled by Neolithic farmers.
2) Paris has attracted a lot of foreigners for many centuries, including a lot of Italian people who may have taken French surnames over time.


http://www.eupedia.com/europe/european_y-dna_haplogroups.shtml