Per records on Joseph Hooten:
1810 census: https://familysearch.org/ark:/61903/1:1:XH29-63R 1817 Tax records: https://www.familysearch.org/ark:/61903/3:1:3Q9M-CS3J-CQQ2-G 1820 census: https://www.familysearch.org/ark:/61903/1:1:XHL5-BWX
Joseph is the only one who stayed in Allen County, Kentucky. By 1820 many of the family have moved into Tennessee.
Since Joseph is in Allen County, I believe that Emanuel Hooten, who lived most of his life in that area is his son.
https://www.familysearch.org/tree/person/details/GSZ7-RTS
This person obviously belongs to a different family.
Elijah was never in Pennsylvania, so how could he have a son born there?