MCP16301 fail on power up - Vin shorted to Vout
PCB was powered by connecting an alligator clip (not a proper switch)
  and there was a small spark. Power source is a Chinese lab power
  supply.


I've seen this problem before on switching regulators and I suspect that the answer may lie in the inductance of the power supply and cable feeding the chip. On connecting the alligator clip there is an "inrush" current to charge the input capacitor and feed current to the load. That inrush current will reduce quite rapidly and, any parasitic inductance in the supply feed wiring will produce a kick-back voltage that may take the input voltage above the absolute maximum limit of 30 volts.

When the load is not initially connected, that inrush current will be smaller.

The situation I saw it on was when an LC filter was inserted before the regulator and I was performing an output short circuit test. The test showed that the switching regulator was current limiting (as per the specification) but, on removing the output short, it fried. I correctly realized it was the input inductor and lived without it.

You might try adding a 27 volt zener diode across the regulator power input terminals.