Will the arduino power autoselection logic short the regulated 5V and the USB 5V?
If you connect a power supply directly to 5V pin on gpio it bypasses voltage regulator hence your board may be damaged if the power supply generates  spikes. But you can power it using 5V supply directly to 5V pin provided you are using a good quality power supply. If you are supplying the power via Vin or power jack there is additional voltage regulator in path giving extra security. Thus you need more 6.5v so as the output of the regulator is 5v. If you supply 5v to Vin the output is nearly 4v thus the board doesn't get enough power.