Yes, this is indeed the same family.I have a lot of info on this family, and even a lot of old photos.My Eli Dougherty (brother to your Allen) was married to Roseanna Christy. They also had another brother, James Harvey Dougherty, who was married to two of Roseanna Christy's sisters (one of them died giving child birth and he ended up marrying another sister!).
These three brothers, James, Eli, and Allen, were all in the Civil War.Eli and Allen look like twins in the photos I have of them when they were older.I have pics of many old "reunions" in which they are both in.
Would love to share info.
Eli is my gg grandfather, my ggrandfather was Clay Dougherty, and my grandfather was Leonard Dougherty.