Yeah, some ideas may be a bit far fetched, but let me defend them:
* Did you read the part about adjusting the production and turns? I was thinking about something like every 100 (or more) turns a +1 production bonus up to +3, and keep the -1 food. So it would actually only be a bit better than workshops now, but with the big difference being that you actually have to build them in the beginning.
* I dont't think this would be unbalanced. In a full game where every hill tile is mined, how many metals pop up on average? Almost all hills are mined but workhops will never be that comon so it wouldn't be like metals will be popping up all over the place.
I think you can allready get some combinations with the current mining system that you cant get from the map generator, and most metals can allready exist on grassland and plains, so it wouldn't be a very big change.
But you do have a point concerning flood plains and building on existing resources, which shouldn't be allowed then.
It would also add a bit more strategic depth because you could actually do something about having no metals in your territory, but then again you do need alot of luck.
* It's the least original one but hey, I'm glad you thought this one was OK