Mini PCI Express Pin Usage
That means as long as I use USB signals on the mPCIe connector, I am conform to the PCIe standard, although I don´t use PCIe?


Yes, as you are not obligated to implement the full sets of mPCIe connections. A good portion of manufacturers have implemented usb only slots, while another portion tend to have two slots per board, one full and one usb only, due to its convenient connector for internal, modular usb devices (wifi, bluetooth most common).