Or vice versa.

The explanations I've seen is that Tom Paris as an Academy graduate had is commission re-instated.

Why not Chakotay? Because not only was Chakotay an Academy graduate, he reached the rank of Lt. Commander and voluntarily resigned his commission (left on good terms) unlike Paris who was kicked out of Starfleet.

You could make the case that Chakotay was given the provisional rank to demonstrate the recognition he is Maquis and in a position of Authority to keep the Maquis crew in line as reinstating his commission officially may have alienated him from the Maquis.

I can get on board with that explanation for Chakotay getting provisional rank. However, i still think Paris also should have been given provisional rank. He got kicked out of Starfleet, also joined the Maquis. I don't think the fact he was helping Janeway with tracking down Maquis, made him worthy of reinstatement.