Keep in mind also that all luxuries and strategic resources on hills require mines and provide substantial gold + cog bonus when worked. You will still be wanting to build some mines with the Incas, however your food production tiles will all be giving you cogs as well. They can well become an industrial powerhouse with the right religion.
Personally I like that mountains will remain inaccessible and only citizens can work them. It will be too much of a hassle to structure the game so that when someone conquers an Inca city they can still use any improvements/districts built on mountains.