First it doesn't really matter what Starfleet wants. Janeway, as Captain, is in the Delta Quadrant and has the power to appoint provisional ranks. Star Fleet can't do anything about that and, based on Life Signs, she is not interested in 'towing the line' about the Maquis but instead asks Chakotay for his advise on how to respind. She does not turn to Tuvok.
In addition she.could pick whatever XO she wants and, in hindsight, demote anyine she wants. See Tom as an example in Thirty Days. At no time does she pull Chakotay's status as XO, even when they disagree as in Scorpion and Equinix. She repeatedly says she trusts no one more. Yes she consults Tuvok, as she consults B'elanna, Neelix and a few others over time. I'm not disputing this, nor that Janeway is close friends with Tuvok. But he was not, and according to the show, ever considered for the position of XO. In fact, despite being so close, she had a different XO for the journey. Tuvok was, even then, her security officer. Star Fleet did not elevate Tuvok to XO status despite his years of service.
Secondly Tuvok can preform all the tasks mentioned above except perhaps the most important one, acting as a conduit between Janeway and the rest of the ship as well as offer emotional support and advice to the crew. Frankly imo Janeway was smart not to pick Tuvok and not just because of the Maquis. A huge part of the job as XO is, in Janeway's case, working on crew relations. In Janeway's situation that is doubly important. Janeway admits right at the beginning in The Cloud she is unsure of her role regarding connecting on a personal level with the crew. She decides she needs to keep her distance as Captain so she desperately needs her XO to step up to the task and act as an intermediary. As such she often asks Chakotay how the crew is doing. Equinox is one example, as is Night. Chakotay has a healthy enotional connection with the crew. They come to him with their emotional needs as in Remember and Nothing Human. Tuvok can easily perform all the other functions as XO, no question, but he cannot connect on an emotional level with his crew. He is a Vulcan. He simply is not equipped to do so. I can only go with what is shown on screen and this is shown in both Resolutions and Learning Curve.
It is true that once she withheld info about Tom from Chakotay but it was not because he was Maquis. She clearly tells Chakotay she did it so he would react genuinely and not give the slightest sign it was a set up. Since Tom was going to deliberately make Chakotay the one to 'push his buttons' to leave this made sense. Chakotay even accepts this when it is explained to him.
Lastly, If Mulgrew wished for more with Tuvok and less with Chakotay then it proves my point. The character of Janeway turns more to Chakotay for advice. Disease expresses this perfectly when she says Chakotay has her permission to express his opposing viewpoints, Harry does not.
Perhaps it could have been written differently but it was not and i can only go with character. Actors and actresses have their own agendas. It doesn't really play into what i tbink of a character at all, even if they are jerks in real life. Look at Russell Crow. Love the characters he creates on screen, actor is a big meh for me.
Hope i answered all your questions. If hate is too strong a word I apologize and will substitute it with dislike.
