The chronitons Kes absorbed in the alternate future caused her precognition in "Scorpion" and her time-traveling abilities in "Fury."
Neither she nor any other Ocampa displayed any time-related abilities, sans "Time and Again" where she merely sensed a change in the timeline. The Krenim's chronitons in her body were activated first by the Doctor's Biotemporal Chamber, and then again months later by Species 8472. The "Before and After" timeline was just another one of Annorax's drafts
Really, how likely is it that Janeway and B'Elanna would die by a friggin' exploding console, after all they'd survived so far? This timeline was just one of the many created and destroyed by Annorax, as he tweaked with history over and over.- Although this timeline did eliminate Janeway for him, Annorax still went back on it because even he was squicked out by Harry marrying his best friend's daughter.
Harry was absent for Linnis's upbringing.
He was a prisoner to the Krenim, or stranded on an asteroid, or in a coma or something. He first met her when she was an adult, and fell in love with her before finding out who her daddy was. Harry and Linnis fell in love during one of the many shipwide-amnesia incidents.
During this timeline's version of "The Killing Game," "Workforce," or some other such incident, they fell in love without remembering their previous history. Once their memories were restored, they stayed together despite the awkwardness.- It may even be that Linnis entered her Elogium and conceived Andrew under such circumstances, and she and Harry stayed together after their memories were restored partially for their child. Linnis does express discomfort with being a mother in "Before and After."
Neelix was promoted to Security Chief because he was considered the most expendable crewmember.
You got a better explanation? Ocampans form telepathic mating bonds that can mix badly with non-Ocampans.
This explains why Tom is so OOC in the time periods when he's married to Kes, as well as why Neelix's character changed so much after she dumped him. Both are oddly obsessive over her when romantically paired with her, and their personalities are drastically different when they're partnered with her as opposed to just platonic friends. A telepathic bond would also explain why Ocampans so easily mate for life and experience no jealousy (when bonded to other Ocampans). Tom was just trying to make Kes feel better.
He wasn't hypnotized or that OOC-gaga for her. He was just trying to keep his senile, dying wife as pacified and happy as possible in her final days. Kes Took a Level in Badass in the Year of Hell
In the original timeline, Kes's personality changed drastically during the Year of Hell. (Recall that a year for Kes is like a decade.) Nonstop battles and losing two close friends made something in her snap. She became more rough around the edges, growing from a "fairy princess" type into more of a "Jedi," and growing into a more compatible match for Tom.