Post your fan theories for Boyhood here!
Samantha is not Mason Sr.'s child.
This would explain why she has dark hair and a dark complexion despite both her parents seemingly being fair-skinned and fair-haired. Olivia's and Mason Sr.'s initial courtship is hinted to be rather wild and it's possible she was already pregnant when she first slept with him or perhaps cheated on him (they were never married anyway, and might have had break-ups or estrangements) but when she decided to stay with him, which lasted at least long enough for them to conceive Mason Jr. together, she claimed Samantha was his. He either believed her, or he secretly suspects she isn't his, but wants to love her like a daughter, hence a few scenes with her that could be interpreted as "trying too hard." In some scenes when he's with both kids, he seems to focus on her to the point where Mason Jr. is almost ignored (their grandmother also seems to give her more attention, and isn't a big fan of Mason Sr.; maybe she knows that Samantha is not his?) but he rarely seems to talk to her one-on-one and his heart-to-hearts with Mason Jr. are much more comfortable and relaxed. A later conversation hints that she rarely speaks to her "father" anymore. Perhaps on some level she knows he's not her real dad.