My personal feeling is this is what happened:
In the 90s NOA started to gain more autonomy/power. Yamauchi, unlike Iwata or Miyamoto was a businessman, not a developer and and having a strong American division for American sales just made sense to him. Who cares if the game is made in Antartica as long as it sells? I think that was Yamuachi's thinking.
However I think at Nintendo amongst the developers/board elite ... they quietly resented NOA becoming more of Yamauchi's darling.
Yamauchi heaped massive praise on Donkey Kong Country, which effectively turned the tide of the 16-bit wars in Nintendo's favor. And again, GoldenEye probably saved the N64 too. And Rare was given far more freedom to do things like the M-rated Conker's Bad Fur Day. NOA was allowed to do things like Nintendo Sports, greenlight Starcraft 64, and sign deals for Star Wars games and the like.
Yamauchi also personally inked the deal with US-based Silicon Graphics for the N64 chipset.
When Yamauchi/Lincoln/Arakawa retired though, Iwata being part of the Japanese development fraternity alongside the other Nintendo Japanese suits consolidated their power and started basically forcing all the Western elements of Nintendo out.
