There's a pretty big difference between a smart AI and an AI with bonuses.
Take chess as an example. A smart AI is one that can make the right moves to beat you. If you play as white, and the AI plays as black, and you two start with the same setup, the chess bot will likely lose to you on lower difficulties, and beat you on higher difficulties, because an AI on high difficulty is really good at chess. Its not getting bonuses, just playing better than you.
If I were trying to design a chess game as an amateur programmer, I would not be able to create a good AI, so if I wanted my chess program to have a good AI, I might have to adopt the civ model. Pretend I'm good enough at AI I can program it to move pieces, but it can't look ahead, so all I tell it to move randomly, but always take an opponents piece when the piece is in range. On higher levels, I might need to make rooks and bishops queens in order to get my AI to be a challenge for humans to beat. You can have better strategy, but the game is unfair, so its up to you to exploit my AI to lure them in to stupid traps to win.
Clearly, the first AI difficulty setting makes for a better game. However, Civilization is a far, far more complicated game than chess (especially for an AI), and being able to get the AI to play the game at all, let alone in a coherent way, is a decent accomplishment in itself. The goal of creating the AI is to make it so that they need as few queens as possible to defeat a human player on the highest difficulty settings, but that's unrealistic with such a complicated game, so we settle for AI bonuses instead of intelligence.
Hopefully Civ VI doesn't need quite as many bonuses for the AI to be competitive, though. That would make it a more fun game, and keep the immersion a bit better.