I don't think they're the same person at all... in any terms - physically, spiritually, whatever. We see in an earlier episode that Abbadon talks with Naomi about the team she's getting to go to the island (Farraday, Lewis, Lapidus) so I concluded he must work for Widmore as well. It's possible that he has access to time-travelling means and that could be why he was there when Locke was born. Or, he's just immortal b/c of island happenings (see below).
Alpert is an "other", a "hostile", what-have-you. And I believe that he does not age anymore. In the episode "The Man Behind the Curtain", Ben says to Richard, "You remember birthdays, don't you Richard?" To me, this says that Richard doesn't age anymore. Which would make it possible for him to look the same at his visit to Locke as a child as well as Ben as a child and to "us" in 2004.
Just thinking thoughts...
