Listen, I know it's a stretch. Emily is a pretty common name. Plus, the character doesn't look at ton like Lee or her other daughter, Flora. But hey, there's a lot of evidence that could support this theory.
Lee said she had Emily when she was 17. We know the real-life events Roanoke take place in 2014. And though Lee never said her age, you could guess she's in her mid-to-late 30s. If she had Emily in the mid-to-late '90s, Emily would theoretically be in her early 20s by the time Apocalypse starts in 2019. And judging by the portrait, it kind of matches up. And, I mean, if Lee had her at 17, we're assuming Emily has a different father, which might explain the discrepancies in resemblance to Flora and even Lee.
All I'm saying is, we never got any sort of closure on that story, and it definitely stuck out as something important when Roanoke aired. And it is strange that there's still some mystery surrounding Apocalypse's Emily. Is it a reach? Completely. But stranger things have happened on American Horror Story.
As for what kind of significance this connection to Roanoke might have? That remains to be seen. You have to admit, though: it would be another cool addition to the tangled web of connections woven by the show so far.