I think the AI cities get a bonus on top of the default yield, in return for not being able to reroll for better positions.  Of course this means sometimes they get better results than a human starts with.  Of course, you can just take over their cities.

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I have never liked the AI getting better settle spots for their capital (and sometimes later cities I believe). It inevitably means that the favourite cities I have built end up being overshadowed by captured enemy cities. Maybe it is just me but I would like my cities which I have invested time into building up to end up the best, rather than the optimal strategy always being to take enemy capitals and make them into your powerhouses.

It also breaks my immersion - sure games like Civ4 and 5 cheat but it isn't usually in blatantly obvious ways, whereas in FE/LH there are many obvious ways where the AI is plainly playing by different rules from human players.