Might just be splitting up versions in modern shipment approaches and older ones was different, today we see a third version as separate title but it wasn't such the case back then over 20 years ago so it's just the case that all titles of Gen were probably just tracked as one installment. VGC has separate sales for Yellow and Crystal but I can't find actual figures for those two by themselves so can only really go by Famitsu 2008 chart for Gen 1 and 2.

So according to Famitsu Top 300 1999.
Pokemon Red/Blue/Green was at 7.9M while Yellow sat at 1.75M
In 2000 they combined that to 9.98M, while Gold/Silver got listed at 6M
In 2001 RBGY hit 10.08M GoldSilver at 6.09M
In 2002 both are not listed anymore

To add on that:

In 2002 Crytal gets listed at 1.85M

So combining all those we get 18.02M
Nintendo says they shipped 23M of RedBlueGreenYellowGoldSilverCrystal.

I don't know if they counted the Virtual Console in that.
Seems insane that there are 5M copies of Pokemon somewhere that Famitsu did not track.

I also doubt 5m was sold on VC considering the release was in 2016 the year Sun/Moon released as well, that 23m figure by Nintendo kind of also backs VGC who can't track digital but have RGB at 10.2m and yellow at 3.1m while G/S at 7.5m and Crystal at 1.3m which comes to a total of 22.1 which given the margin of error and the official shipment from Nintendo indicates VGC were either on the ball with their tracking or had an ultra reliable source.

On another note it's possible VC numbers were added.

VGC did no software tracking before the seventh generation, so the DS and PSP are the earliest systems when it comes to tracking. All software numbers for preceding consoles were derived from official shipment data and other sources, including news articles where numbers of official trackers were published.

Discrepancies between Famitsu and Nintendo's shipments are nothing new, just look at hardware. Nintendo has the 3DS at 25.24m shipped for Japan alone, but Famitsu's sell-through isn't close to that despite it being clear that retailers don't have much stock left anymore at this point in time. The Pokémon numbers we are talking about here date back about two decades and Famitsu being less accurate back then they are today is very much possible.