Janeway had the authority to promote Starfleet officers under her command, but not the authority to recruit new officers. Hence the "provisional" part. But the situation required it so all the Maquis she integrated wore those alternate pips until Starfleet could ratify and approve them (most, if not all of which, they did.)
But didn't she recruit Tom Paris? Or did she just "restore" his rank of Lt? If she had the authority to restore a criminal's rank, surely she would have had the authority to recruit, either way.
Paris graduated Starfleet Academy, and had a rank before being jailed. They don't say it outright, but I think Janeway got Starfleet's permission to commute his remaining sentence in exchange for being an "observer" on her ship. But even without being part of her crew officially, he was part of Starfleet again (uniform) so she had the power to promote (and demote) him at her discretion.
Ah I think you're right. I think she says that at the prison colony, that he'll be free to do whatever he wants in exchange for guiding them through the badlands.
If it makes you feel better, Captain Chakotay had normal pips by the time the Protostar was commissioned. Guess Janeway just didn't want to grant ranks away from Starfleet proper.
I just always imagined an awkward conversation between Janeway and some new species she had just beamed on board: “so uh, Captain, why do some of your crew have different rank pins?”
“Oh, you mean the terrorists? Don’t worry about it, they’re fine.”