>>53267330A lot of Pokemon had their official colors changed in between the release of Gold/Silver and Crystal, because Sugimori didn't like the palettes on their official artwork and changed it. These color changes were strictly retconned and never acknowledged in every form of media besides the the sprites of original Gold/Silver. Sneasel is the most well-known, but some other Pokemon like Sunkern and Bellossom were also hit.
Something like this could well have been the case for the different Shiny palettes in Gen 2, but we also know that the Shiny colorations in the Gamecube games were also pretty different from their 2D sprites. I think it's most likely that earlier installments of the series just didn't care as much and shiny colors weren't canonized until around Gen 4, where we stop seeing inconsistencies like this. One of the designers for the newer generations (I think James Turner?) mentioned being allowed to pick the Shiny colors for one of the Pokemon they had designed, which implies that specific Shiny colors are an active design choice nowadays.
