So, I didn't want to use the Bluetooth mini receiver, and wanted to use my wireless keyboard and mouse in the USB mode (no OS bluetooth support needed; everything is done in hardware). All I had to do was comment out the lines related to Logitech devices in:
After that, I was able to use mx5000-tool to change a few of the LCD screen views. Not to mention, I can remap CAPS LOCK to CTRL and it won't beep each time I press it. Whatever.