The chocobo forests looked artificial from the outside.The chocoboys treated these forests and decided to perform experiments on them.Genetic manipulation was made on some animals to create mutations.The time traveling and GPS orientation characteristics were implement genetically on these animals.
The GPS probably become some innate pattern on the Chocobo´s brain.
Where is your proof or even a reason that would make you think that the chocobos were being genetically manipulated? I mean unless you have some proof then there is no reason to believe you.

All of the chocoboys had the same appearance.That´s because they were all shumi´s who became possessed by the same person-Hyne.And they look like Hyne.
As for the choco boys all looking the same, its because they are the same person. There is just 1 choco boy and he travels between the chocobo forests using chocobos so he isnt some shumi he is just a normal person.

Plus how can Hyne possess like 10 different people at the same time? I mean if you are in 1 persons mind how do you go and get into another persons. There is no way to simultaneusly possess multiple people.

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