Samuel Henderson - Was Samuel descended from the Hendersons of Fordell?

Here's part of an email from @David E. Henderson, on 2017-03-16 (my notes [inside square brackets]):
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I am 858 Thomas Edward in the [Clan Henderson Society] Consolidated Tree. That line ends with [ie. leads back to] Samuel Henderson b. 1713. The family genealogy I received from my great aunt, and a variety of sources working on this over the years have indicated that Samuel’s parents were William Henderson b. 1676 and Margaret Bruce b. 1680. William is reported as the son of Sir John Henderson of Fordell. That is the line I grew up with and what I have spent a lot of time researching.

I thought I was making progress when I found the birth record for William showing him to be the son of John and Madeline Lundie. That would prove my link to Fordell if it were true. However, my DNA is about 4000 years off from that of Alistair [Current Chief of Clan Henderson.
https://www.geni.com/people/Alistair-Henderson-of-Fordell/600000005...
His line back to Fordell is well researched.]. The mutation that splits R-A2 occurred 4-5000 years ago. There are a number of significant and well characterized mutations that separate my male line from Alistair.

At this point I don’t know if the name William and Margaret are correct for my line and refer to different people or if the names are not even correct. People have looked for names in the records and attached family lines to whatever they found that was close. It is, of course, possible that John was not actually the biological father of William, but the fact that the name Samuel was not used in christening records anywhere in Scotland in this period suggests that Samuel was born in Ireland rather than Scotland.

I also did an analysis of other last name matches using Scottish census records to determine where there was the greatest overlap of all my surname matches, Patterson, Allyson, and Ellyson. That leads me to believe that my ancestor lived in the Scottish lowlands before surnames were common and fathered these different family names. My Henderson ancestors would then have been caught up in the move of people to Ulster Plantation and then come to America in the early 1700’s.

I have pretty much given up hope of finding anything in Ireland. But we do have 15 male lines in the [Henderson] project [at FamilyTreeDNA
https://www.familytreedna.com/groups/henderson-dna/activity-feed] that share a common ancestor with me in the past 500 years. So I hope at least to help this group make some sense of things. I also know that many of the immigrants to Augusta Co, Virginia where my ancestors lived came on ships that did not keep records of immigrants. So even finding the ship is unlikely.
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