OK - I admit I am now clutching at straws but I am going to throw out a possible scenario for consideration - call it creative thinking!
What if one of the Thorne boys got a girl pregnant, she had a baby and the Thorne family brought her up as their own? perhaps the girl died, or it was a convenient arrangement. In that case the child would not have been registered initially as a Thorne, or would she?
The reason I have wandered along this path is that Francis William has gone missing on the 1891 census - did he ever appear again? There is no record of a death for him, and he would have been around 14 or 15 at the time of Eunice's birth - old enough to do the deed, but probably not old enough to have been a good father. Eunice named her father as William (wheelwright) on her marriage certificate and didn't change this. Is it possible that Francis William was banished by the family somewhere? Perhaps he went to sea, or emigrated to America or something?
I also notice that Eunice was named as Priscilla on the 1891 census, and not her own name.
Like I said - I have no concrete evidence and am just thinking "outside the box" to see if it helps solve a puzzle.