Why is Seamus McFly married to a woman who looks exactly like his great grandson's wife?

Obviously, they used the same actress just to make one joke work.
But in-universe, it is apparently because the McFly men all like women who look alike.

In a 1990 issue of Back to the Future magazine, Robert Zemeckis and Bob Gale answered frequently asked questions, including the one you asked.

Q: Lea Thompson plays Maggie McFly, Marty’s great-great-grandmother, as well as Lorraine, Marty’s mom But Lorraine’s family name is ‘Baines. ’’ Why did Lea play Marty’s paternal great-greatgrandmother, when she’s really not part of that family? Is there something kinky going on in the history of the McFly family?

A: Lea plays Maggie because we didn’t want to make a Part III without having Lea in it, especially in a “Mom is that you” scene! Of course, we thought about whether it made any sense — obviously, Maggie McFly and Lorraine Baines cannot be blood relatives. But we did come up with a satisfactory answer: It’s a well known adage that “men are attracted to women who remind them of their mothers.” Clearly then, when Seamus married Maggie, that insured that the McFly men would have a genetic trait that attracted them to women who bear a resemblance to Maggie or Lea Thompson (even Jennifer is the same physical type!)