Do you skip an eliminated player’s turn with Altar of the Loa if all they have left in play is a fort?
No. That player will count toward the endgame condition because they can’t give move actions, but assuming there are enough other players still going to prevent that, the player with the fort still gets their turn in the normal sequence. If there’s nothing within range of the fort to attack they won’t have anything to do, but that’s not enough to skip them entirely.
Can it skip that player if they didn’t have a fort? (absolutely no units in play)
That’s a discretion call left up to the person running the event and/or the group, that’s best decided beforehand, if possible.
If the “eliminated” player steps out entirely and forfeits it’s easier to justify skipping them, but if they’re still in contention to win based on previously-collected gold, they’re still part of the game even if they have nothing left to do during their turn.