@TMIT: That's what I thought too, but for the most part the player pays normal costs, while the AI gets a discount. The exception is research, where the AI actually pays the normal value, and you pay 125% of the cost in beakers. Which is basically the same as the AI getting a 20% discount compared to the player.
(EDIT: Still, as far as player experience is concerned, it FEELS like you're getting some penalties tacked on you on Immortal. As far the game is concerned it just got rid of the bonuses you had for lower difficulties, but taking away a benefit and a disadvantage feel exactly the same. On Emperor the player actually starts with a slight unit discount compared to the AI, because the player pays 80% of unit cost while the AI pays 85%. The era bonuses quickly get rid of this advantage, however.)
Although it may be possible some of the bonuses to production stack. It depends on what some of the xml values I couldn't identify are.
I think what accounts for a big part of the bonuses I wasn't seeing is the iAIPerEraModifier. It's -4 on Immortal, and -5 on Deity. From what I understand now, it is an additional discount applied across the board for production, city maintenance, etc., but NOT research. It starts at 0 in Ancient, and then increases for every Era after that. By the modern era, it adds up to an additional 25% discount, on top of the normal 20% on Immortal, or 40% on Deity.
Good thing it's applied multiplicatively on top of the normal bonuses, and not subtractively. So in the modern era unit costs for the AI on Immortal would be 80% * (1 - 25%) = 60%, not 80% - 25% = 55%. Deity's costs are 60% * (1 - 25%) = 45%, not 60% - 25% = 35%.
@vranasm: Researching Superconductors in 1340 AD? BWAHAHAHAHAHAHA! Now that's what I wanted to see.