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

Wouldn't hurt.
Promini & duemilanove from 2009 designs had hardier regulators - I have been running 14 promini's with external 5V since Jan 2010 with no issue.

It was the change for Uno & Mega when this started occurring.
Since many clones are coming out now, wouldn't hurt to read the spec for the regulator used if you can determine what it is. Or just play it safe and add a diode.