For example, in HG/SS, if I went into Cerulean cave, and my RNG happened to generate a Shiny Mewtwo, would the Mewtwo (which I have NOT started battling) be green like it's shiny, or would it still be purple?
Another example: Say I have the Blue Orb (HG) or Red Orb (SS) and I go to Embedded Tower. Would the unencountered Kyogre/Groudon be Purple/Yellow, or is it still Blue/Red?