That is such a good question, unless someone had the fence turned down or off and that is why he was able to get through...

In Answers the producers said that Smokey scans people and then they said the Island can create the apperations.. Maybe they are not exactly one in the same either... Maybe Smokey just collects the info and in Eko's case does the dirty work but the apperations are something else..

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Please don't give up, Des. Because all we really need to survive is one person who truly loves us. And you have her. I will wait for
you. Always. I love you, Pen

DESMOND: I love you, Penny. I've always loved you. I'm so sorry. I love you!
PENNY: I love you too.
DESMOND: I don't know where I am, but--
PENNY: I'll find you, Des--
DESMOND: --I promise--
PENNY: --no matter what--
DESMOND: --I'll come back to you--
PENNY: --I won't give up--
BOTH: I promise. I love you.