It's amazing isn't it. Your dna matches are so interesting.
I don't think William and Ann Brewer of Lancaster County (1800) are John's parents. If the Brewer/Lanier researchers are right, it should be as you say and John is Lanier Jr.'s son. William must be an uncle or something, and Lanier Jr. has to be the father of John (Joseph's father). Besides the powerful dna results, the dates match. These are my thoughts about it.
The only thing I didn't see in the online files is proof in the way of a will or something about Lanier Jr.'s children. I haven't read the Brewer books that are mentioned in various posts; maybe there's documentation in them. But either way, I'm sure the families know who Lanier Jr's children are.
I was wondering...do you know if the mother of John, Wiley, and Cornelius has an influence on the matches? If she does, would it show which sons had the same mother?
As for Phebe and John, a marriage record for either of them would be great. Maybe another type of record will show up too.
I wanted to thank you for accepting my idea that Emberson Brewer who married Elizabeth Counts is most probably a brother to Joseph. Someone in my line might have to have a dna test eventually too, for the proof.