Well, Darkrai is a creature who brings nightmares to reality, yes? Well, in theory, somebody could absolutely dread Darkrai itself, meaning that if Darkrai came to them, there would be another Darkrai as a result. In another theory, since it's likely that few have seen it, one could imagine and dread it, but in incorrect colors, thus creating shiny Darkrai.
Dialga is another Pokémon of time, meaning that it, like Celebi, could theoretically traverse timelines. Maybe even travel into a timeline where Arceus decided to create it in an alternative color. This would cause shiny Dialga to exist in another timeline.
Palkia is the space Pokémon. If I remember right, it could enter other dimensions and worlds. With that in mind, similarly to Dialga's alternative timelines, there's a chance that Palkia's colors could be different in this other world. This means that shiny Palkia exists somewhere.
Giratina was banished into another realm at some point. There's a possibility that in some timeline or world, this caused it to change in color due to its new environment.
Latias and Mew can literally change their appearances. They're shiny because they want to be. If I remember right, Latios also has the reflective feathers like its somehow smaller counterpart, but I can't exactly recall.
