Regarding the Maquis pips, I agree everyone should have used the Starfleet ones. It was clearly an out-of-universe way to tell the audience 'these are the Maquis crewmen'. In-universe, the only thing I can think of is that since none of them graduated from the Academy, it would be 'improper' for them to wear actual pips.
Which brings me to Chakotay and Tom.
Since he did graduate and he was booted as a lieutenant, Janeway simply restored his status. Another reason... Paris was the only former Maquis who was not on Chakotay's ship.
Chakotay is a harder one to figure out. By all rights, he did the honorable thing and resigned and then joined the Maquis, which means he still had good standing in Starfleet, since he didn't go the traitor route that Eddington and Hudson did. (Despite being labeled a criminal and Tuvok being tasked with bringing him in.) Resignations can be overturned, as we've seen it done in the past. (Picard granting Worf his commission back in "Redemption II".) Maybe it was a request by Chakotay himself... a way of showing his Maquis people, at least at first, that while he has adopted the Starfleet way again, he still will represent the interests of the Maquis crew.
Eventually, everyone should have had regular pips. Unless Janeway felt that unless she got full authority from Starfleet pardoning each Maquis crewman, she couldn't give them the full status of a Starfleet officer.
But that could have been a nice side story in late season 6 or in season 7... with regular contact being made monthly with Starfleet, Janeway could have fought for those rights and pardons to be given.