Where did the Auditore and Kenway lines merge?

It's well known that Flavia Auditore (1513 - Unknown) is a direct ancestor of William Miles (and therefore the Assassin's Creed present day protagonist Desmond Miles).

We also know that Edward Kenway is the first member of the Kenway line to be in the Assassins:

Edward will be thrown in the middle of the ancient war between Templars and Assassins. He will be trained by them and finally become the first Kenway member of the Assassin Order. He’s the father of Haytham, Connor is therefore Edward’s grandson.

In other words, Edward Kenway is known not to be a descendant of Flavia Auditore. Neither is Ziio, as a native American in the 18th century. So when did the lines merge?

One theory (mine) is that Tessa Kenway is a descendant of the Auditore line, but I haven't read Assassin's Creed: Forsaken and none of my research suggests that there's any evidence to support this. I can't find any earlier reference to William Miles life than this story from 1977.

Is it known when and where the Auditore and Kenway lines merge to create the Miles line?

As somebody mentioned in a comment, and as I mentioned in a previous answer to a very similar question, it is currently unknown how the Auditore and Kenway lines connect.

As you likely already know, both from your official diagram and from the comments, Desmond appears to be related to the Kenways and Auditores through his father William Miles.

As such, we can focus on the paternal lineage (barring any weird, incestuous connection among Desmond's paternal and maternal ancestors). Beginning with the Auditores, Ezio had two children we know of: Flavia (as you referenced in your question) and Marcello. Although the line in the canonical diagram you posted above appears to be highlighted the lineage flowing through Flavia, in theory Marcello could also prove to be the link (though this is pure speculation, and would require future confirmation by Ubisoft). Nonetheless, both of these children represent the latest known canonical individuals in the Auditore line.

However, to elaborate on the information we do have, we know the earliest instances of the Kenway line are in the form of Edward's parents, Bernard and Linette (both from the Black Flag book). As such, some link could potentially exist flowing from Flavia to Bernard and Linette.

As you mentioned in your question, the link existing through Tessa is also possible: we do not know much about Tessa Kenway or her family tree (beyond her father being some sort of wealthy landowner). Again, since there is a vacuum of information, Tessa being the link is entirely possible. However, based on the current information, the Auditore lineage would have to connect to either Bernard, Linette, or Tessa (and not Caroline Scott, as she is not directly related to Haytham and consequently the paternal lineage).

Unfortunately, with respect to the familial lineage, the sources we have are limited, with the diagram you posted being a significant step forward in the identification process. However, I can point you to this extensive chart which, though not canonical, is nevertheless a useful resource for yourself and others attempting to trace the familial lineages of the Miles family as it is understood today in May 2017.