>>58635033According to Takao Unno (the art director of HeartGold & SoulSilver, as well as the artist who made Lyra), when content from Crystal was being remade, he made Lyra without thinking about Kris’ design from that game. Meaning that in his mind, they are different characters design wise.
The Pokemon Adventures manga is the exception to this rule because they give every protagonist different names from their game counterparts. One Example is that Brendan is named Ruby. You are right about one thing, the manga treats Kris & Lyra as the same character, but at the same time, the manga is a separate continuity from the games.