The Hologram Chakotay was probably written once they took the Janeway/Chakotay pairing off the table. The writers whipped up the Chakotay/Seven pairing out of whole cloth and didn't derive it from normal character development. What you're all saying makes sense, and the pairing would have worked had it been properly developed, but what the writers wrote didn't work.
Granted, with how the story ended up, the writers make sense if you're willing to accept their idea that Seven suddenly wanted Chakotay near the end of season seven in "Human Error" when for three years she didn't give any indication that I can remember as to her wanting him.
I believe in attraction at first sight, and gradually building attraction over a period of time but not... no attraction for years and then suddenly wanting someone's babies. That doesn't fly with me. By contrast, with the Paris and Torres relationship, one could see it gradually build.
Seven didn't show her emotions much, true, but you also can't expect someone to believe, "She grew to love him over the years and never showed or hinted at anything other than a professional relationship to him or to the audience until Human Error." It might be repressed emotion, but it doesn't look like it. It just looks like bad writing.
I'm sorry, I'm just a stickler for proper character development and I don't like characters doing things out of the blue like that. It wouldn't have been too much trouble for them to say that she developed feelings for Chakotay over the years secretly. Just mentioning that once would have been better. I'm not angry or anything, I just like to analyze plots and characters.