When I first heard about the "overbuilding", I was thinking that it would be something more akin to the old building still being there on the tile to give you yields. So basically you are allowed 2 "active" buildings on any tile, but anything that's not active anymore still gives you an underlying yield. So if I overbuild my library, I should keep the +2 science on the tile for eternity. I don't know what the balance for maintenance on buildings should be, maybe obsolete buildings should be 1/2 maintenance from what they are now. So you do have a permanent penalty to them, but you also have a permanent bonus.
I kind of feel that would also solve a lot of these annoyances. In that case, you never worry about what you're overbuilding, since the new building just goes on the tile. A Quarter would be any district with 2 active buildings on it. The warehouse buildings would count as active in all eras, but you could still overbuilt the ones from the previous era, but they would still be around and give you yields. So if I build a Granary and a Library on a tile in the ancient age, if I build an Observatory on it in the exploration age, then it would be considered a quarter (Granary+Obs), but I could still actually overbuild the granary too while keeping its yields.