Here is a paper summarizing the suitability of the navigation light rules (Colregs / IRPCAS) for modern yachts. It was written by a World Sailing Working Party chaired by Rear Admiral Chris Oxenbould AO RAN (Rtd). Members of the working party included Stuart Carruthers, Will Apold, Chuck Hawley, and Stan Honey.
The paper suggests changes to the IMO Colregs, to address several areas where the rules are out-of-date and most sailboats over 20m are equipped in violation of the rules.
Note that the paper also recommends operating two sets of running lights simultaneously in certain situations (paragraph 108), and recommends the use of a masthead flashing light in certain situations (paragraph 98). These practices are good seamanship and are in compliance with the current navigation light rules.