They may not have caught Jon in the geneology records because he is only 71, so he would not have been listed in the 1930 census (the last one released, as there has to be a 72 year gap between the census and its release to the public, due to privacy concerns.) I found the name in some of the family-generated family trees of families just doing their geneologies - he was probably put there not by records search but by family members who knew.
I think the geneologies specifically done on Obama were probably made by those who didn’t know the family, so there will only be folks listed in public records (ie census data), unlike family-generated geneologies where families talk to each other and recall who was married to whom and “what where the names of Uncle Rolla’s kids”.
So it is established that Jon is a great uncle, it sounds like.