It's his uncle. He can't very well invite his maternal aunts and not Earl Spencer. That would give the press a field day with an endless ream of suppositions.
I wouldn't anticipate there to be a rift as such, rather, there's never been any public held occasion apart from the memorial or concert held for Diana, by where we would see them interact. Who knows what kind of correspondance they have. Only they know
The Spencer's have as much of a right to be there
(not that you were suggesting they don't) as William's paternal relatives and I was glad to note that they are seated behind Catherine's immediate family. An appropriate seating arrangement, I thought.