It does seem an odd situation. 5V is made available on a header, from a boost regulator even, with 4 other signals that are 3.3V level parts and
have a limitation of "Voltage on Input Pins with Respect to Ground...... ..............................-0.3V to + 4.0V"http://www.atmel.com/Images/doc11057.pdf
One would have thought a part such as TXB0104 for signal level translation might have been standard here to avoid any damage from 5V signals on the header.
Many parts still run on 5V, so it's nice having a source, but the parts need to return 3.3V signals. Connecting up a MAX7219 for instance, 4V-5V is needed for a supply, 3.5V is needed for a minimum high at 5V, so level translation would be needed.