There's a popular fan theory, particularly among Jott anti-shippers, that Rachel is Logan's daughter, not Scott's. It stems from a scene in
Days of Future Present, specifically
Uncanny X-Men Annual #14, where Sue Storm and Scott are turned into Hounds by Ahab. Sue is able to sense and track Franklin while Scott can't sense or track Rachel.
During a Jay and Miles Explain the X-Men podcast recorded within the last couple of years, Claremont revealed this was a hint of his intent to reveal that Rachel was the child of Jean and the Phoenix Force. That is, the Phoenix impregnated Jean, and Scott, like Joseph in the Christian gospels, was just a stepfather. This was one element of his project post-1986 to deconstruct and retcon away as much of Jott as possible.
After Claremont quit, Harras and his writers ignored this completely and went forward with Rachel as Scott's daughter. That hasn't stopped certain segments of the fanbase, particularly Jott anti-shippers and Jean/Logan shippers, to adopt some variation of Claremont's idea as headcanon.
Canonically, Rachel is still the daughter of the Scott and Jean of her timeline.