Chakotay as XO was really more of a political/PR assignment than anything else. Tuvok would have made a fine Number One, but with 30ish terrorist Maquis onboard, they need to be kept in line somehow. Having their former Captain as second-in-command would see them fall into line behind him.
Shelby may not have liked it, but I think she would do the same thing, so as to install order into the Maquis. Though I do get the feeling she'd address him as lieutenant
commander every so often--especially if were pissed off at him (so probably frequently in the first couple of years).