When I open a project in Xcode 8 (or previous versions) and check the File Inspector, there's a section called Project Document, with a combo box named Project Format.
The available options (in Xcode 8) are
There does not seem to be any major breaking change in this format change (I tried few of my project, nothing changed in the xml structure itself except the version parameter..).
As far as I remember, there were few project formats before that, some of which actually had major changes, but that is probably not going to happen again because that was in the times of major structural changes to iOS, like from iOS2 to iOS3.
Also, just side note, the default for new projects is still 3.2 so it is very likely that 6.3 is basically for testing and version that they will force later will be -7.
My best guess would be that the new format is there for Swift 2 and the way how modules / dependencies are handled in there, as it for sure requires some additional data to be present in the project. But to be 100% sure we would need information from somebody on the Apple Team.
Hope it helps!