Suzuki and Toyota are also giving this outdated interval. In fact, most of the Pakistani awaam is following this wasteful interval. There is no way that the additive pack in modern oils suddenly depletes after 3 months.
Anyways, there is not such thing as Honda engine oil; it is just oil formulated by another company, in this case Total's Quartz 9000. Honda then slaps on their stickers on the bottles, and sells it at their dealerships.
BTW, a Honda can go up to at least 16k km/1 year if not mainly driven under 'severe driving conditions'. Under severe conditions, it comes down to 8k km/6 months (yes, even in dusty conditions). This is the interval followed in the U.S; Europeans follow an even longer interval.
For warranty purposes, you will just have to bite the bullet and follow the 5k km/3 months interval. After warranty expires, feel free to switch to 6 months.