The factory fill is fine to leave in per the exact Honda specification. But, this is a sight for those that offer alternatives and options to what a given manufacturer suggests/advises. In times past if a consumer was to follow what the auto maker suggested in the manual, a somewhat less than ideal maintenance schedule would have been followed. Today, due to warranty issues, consumer laws, and specific automotive requirements, the auto makers give much more detailed and careful instructions for the care of the vehicle they sell.
That said....individuals may have ideas and opinions that differ...while still not voiding the warranty. In my opinion, leaving the factory fill in a new Honda for 5k miles is a sort of compromise for those that cringe at leaving any factory oil in for over 500 miles....and for those (including the manufacturer) that just do whatever the manual says (if even that much). From the miniscule amount of research I've done about the subject, at 5k miles the need for any longer time or mileage needed to properly break-in the engine is zero. I see no harm, nor any second-hand evidence of harm done when changing the FF out at 5k. I also figure that if Honda was honestly worried about the consumer changing his oil out at 5k, they would have stated that it would void the warranty. Being that they did not, and by still giving Honda engineers the respect they've earned, I say 5k is a sound choice.
One thing to also keep in mind is that most manuals, OLM's, and factory maintenance schedules are designed to keep things simple and easy for less-than-superior minded car buyers.