I made that reflection to myself as I writing it up... While food coming from farms/irrigation is definitely natural, the idea that production (what ever that is) comes primarily from mines, and that mines can only be built on hills is rather artificial. But yes, we are used to it, from previous civs and 4x or RTS games more generally. It's ingrained to the point of being intuitive now, might as well stick with it.
In terms of balance its ok to have some bad tiles, its okay to have some medium tiles, and its ok to have tiles that are great at food or production. The problem is that hills seem to be great for food AND production. Better than bonus resources when - the entire point of bonus resources - is to have a few very good tiles that easily stick out.
For what it's worth, I think removing the adjacency bonus for hill farms, or pushing their constructions further into the tech tree are reasonable ways of curbing this problem.