When migrating Pokemon from FireRed and LeafGreen to HeartGold and SoulSilver, the Pokemon are travelling through time, as FRLG took place 3 years before HGSS. This also means that you somehow contacted Red in the past and asked him to send you Pokemon. This all creates a complex chain of events. Migrating from Hoenn is different as Hoenn is a different region and pokemon could be transported electronically to Kanto at the present. It's strange that Prof. Elm is ok with trading these pokemon from the past but not the spiky-eared Pichu.