"Supplying voltage via the 5V or 3.3V pins [...]" to what?

CrossRoads:
See Protection Diodes, page 10
http://www.onsemi.com/pub_link/Collateral/NCP1117-D.PDF

Yep, have looked at that before.

Only when Vin is shorted or crowbarred to ground and Cout is greater than 50 µF, it becomes possible for device damage to occur.

Now according to the UNO R3 schematic, Cin is 47 µF so I suppose that could be equivalent to a dead short if you connect a "live" 5V supply with a large output capacitor to Vcc. Powering up a system once properly connected should on the other hand, be no problem as the rise time of the supply would be limited.

CrossRoads:
Barrel jack may be unpowered and a turned off wallwart could have the effect of being a short to Gnd. Being unconnected would be different - no path to Gnd.

Obviously, if you are going to power via Vcc, you should not have anything connected to the Vin pin. The barrel jack is of course, isolated by a diode.

I suppose in summary, the regulator may well be a bit fragile, but susceptible only to "hot connect" under certain "experimental" connections, should be quite safe for a properly implemented system.