As I walked down the tree row, I noticed significant differences in the diameter of the rootstock as compared to the trunk diameter of the scion (photos above). For tree "A", the Giles rootstock has over-grown the Major scion. Tree "B" has a smooth transition between rootstock and scion. Trees "C" and "D" are more typical of trees grafted with a Major top--the scion overgrows the rootstock.
Major is a vigorous growing tree, often producing the largest tree in a planting of several cultivars. That's why it so common to find Major scions overgrowing their rootstock. However, I wanted to show you these photos to make two points. First, no matter the seed source for the rootstock, there will always be variation in growth among rootstock trees. Each pecan rootstock tree has a unique genetic composition created by a known mother (in this case Giles) and a unknown father (pollen blown to the stigma on a puff of wind). This variation may cause differences in the appearance of a graft union but it appears to have little impact on the scion's performance and yield.
The second point I wanted to make is that is not that critical to plant a particular seed source to grow rootstock trees. In northern pecan areas, you should use seed from either local native trees or nuts produced by a northern cultivar. The resulting trees will have the best cold hardiness for your location. Many years ago, we had some Giles trees growing at the research station that had been propagated by a southern nursery that used a southern pecan cultivar for growing their rootstock trees. In 1989, temperatures dropped to -26 F (-32 C) in mid-December. The Giles tops survived the cold but the rootstock portion of the tree was killed by the cold. With a dead root system, these tree had to be removed.