It's a result of the unification of all inorganic materials during the April 1, 2010 (the 31.01) update. The "metals" list could more accurately be called an "inorganic" list, so unless you could separate stones, gems, and soils from the "true" metals (which you can't) you couldn't remove those materials from the metals list.
I don't see your problem with customizing stockpiles, however; all the "true" metals are invariably at the top of the list, in my experience, so they're easy to find, gems and stones are invariably different item types so if you simply separate out metals from everything else you can easily split metal and non-metal furniture, and if you want a stockpile for only items made of a particular type of stone you can now do that (which you couldn't in 40d) by disabling everything on the metals list except that one type of stone.
If you often wish to make separate stockpiles for metal and non-metal items, do as I have done: make a macro that, when run, toggles every metal on the metal list. To do this, go to a metal list in the custom stockpile menu, hit ctrl-r to start recording your macro, alternate between hitting ENTER and down 26 times (more or less with mods, depending on if they add or remove metals) to toggle every metal on the list, then hit ctrl-r again to stop recording the macro. Now, hit ctrl-s and name your macro to save it. You can then hit ctrl-p to play the active macro (which will be the one you just made), or ctrl-l to load a saved macro as the active macro. You can make a metal-items-only stockpile by going to the metal list, hitting (f) to forbid all of them, then running the macro to toggle all of the metals to on, or a non-metal-items-only stockpile by running the macro to toggle the metals off. Quick, simple, easy.