Regarding Janeway and Chakotay, they had similar moments in Voyager, too. At first she was thinking she’d get back together with her fiance Mark. Then eventually she decides that since she’s a captain on a small ship that’s isolated from the rest of the federation, she shouldn’t fraternize with the crew.

Also though, the two have a tight bond. Think about how long they’ve known each other, and what they went through together. I mean, she had her first officer infiltrate his ship after which they all got flung to the opposite side of the galaxy, and she made him the first officer. A lot of what we’re seeing use just that these two care so much about each other, not necessarily romantically.