Exactly. You can get a board that accepts Arduino shields and lets you program with the Arduino environment, but also natively supports high-speed buses like PCIe, USB, SATA, and Ethernet, and provides a more direct programming environment based on Linux or a smaller embedded OS.
I'm curious, what board in the Arduino form factor are you talking about that can do PCIe and SATA? Those require fairly sophisticated processors AFAIK (read: expensive).
Also, for many uses programming in Linux is the exact opposite of direct when comparing to banging out some bare metal C or C++ on a dinky 8-bit micro. Maybe using a RasPi to blink LED or read a temperature sensor is more accessible to some people and that's a good thing, but it's like killing ants with a tactical nuke.
