The problem is that the inventor Ann is a different character than the inn keeper Ann. The inventor Ann (HM and MM) is named Ann in Japanese, while the inn keeper Ann is Ran in Japanese. They coincidentally shared the same name in English version of the game, but they technically are not the same person. That's why I edited the appearance part in the box to not including MM (Magical Melody).
It is kinda like Maria (in BtN) and Maria (in HM and MM). They are different characters with different appearance, but share the same name. Ann (HM, MM) and Ann (BtN and future games) look awfully similar, but they are different character - not same character with different role as you're talking about.
HM64 Ann is an interesting case, but so are all characters in HM64. But I understand the situation and respect the decision.