Things are generally cheaper when you buy more of them. It’s true that once you pass a certain threshold this isn’t as significant, but that threshold can be pretty high.
Then you get into things like commodities trading (eg buying and maybe even selling futures), which is something Starbucks engages in. It would be very hard for a small shop to participate in commodities trading (barriers of entry due to size, time in the day, etc), let alone do it well.
There’s also a bunch of little things that ar a “do it once for all stores” or “do it once for a single store”. At a mom and pop that usually means that they won’t be able to do it as well as a bigger store because of time and resource constraints.