There's also just an expected amount of waste that you build into any financial models. If you've ever been in a good cafe at opening, you'll see them burn through half a bag of espresso just to dial in the grind every morning.
II think it ends up being less about money and more about what a pain in the ass it is. The reality is the margins on an espresso shot are really good anyway.Our shops only serve a single size shot - equivalent to a double. We never split shots, or serve singles or whatnot. We'll add a second shot to an espresso/milk drink, but it costs the same as ordering an espresso.
It's a workflow issue. Almost everyone pulls shots at a some single, pre-determined, weighted dose you would identify as a "double." If someone only wants half that, the time and effort saved by having the barista pull the same shot they pull for everything and dump half of it out is worth more than the 12g of coffee that go to waste - particularly since almost no one wants a "single" these days.
There's plenty of good green coffee out there if you are willing to pay for it. The reality is the most of the really big players don't bother with the good stuff anyway. Even the bigger specialty roasters aren't operating at high enough volume to corner the market on quality beans.
Metal filters are a pain in the ass to clean, and would really disrupt work flow. Personally I hate pour-over in a cafe setting anyway (too fucking slow), and using metal filters would slow this down even more. That said, you might be a super-taster or just really sensitive to the taste of paper. There's no reason using paper filters should leave your coffee tasting like paper.