You can supply it to the Vin or the power connector but you'll be under powering the unit. The voltage regulator on the board is looking a voltage higher then 5V so it can supply a steady 5V the system. You can easily attach 3.3V peripherals to the unit. Thats why it comes with a 3.3V pin for powering those items.
Yes using you can modify a USB cable to exclude the power and only use the data pins and receive your power from an outside source without effecting serial communication.