I hate to say it, but I think Secret Identity, (whose banner just appeared above me, irony of ironies) did a better job with the "Kid with superpowers lives in a world where Superman is a comic character" concept then the original story did.
No big surprise, since in the trade paperback introduction Kurt Busiek elaborates on how he originally wanted to write a Superboy-Prime story, but in order to get his project approved the concept had to change significantly. I'd recommend reading this intro, since it provides a fascinating inside look at how an original idea evolves to get past DC's screening process.
And recall that Superboy-Prime's "Secret Identity" was completely blown in front of neighbors, friends and police when he and Superman paid a final visit to the Kents and Laurie. Even if the Crisis ended differently and Earth-Prime saved, Superboy-Prime would have a problematic homecoming. Do you really think this story could be kept quiet?
Superman: Secret Identity resolved the dilemma of "everyone knowing Clark Kent is Superman" by turning the concept on its ear -- NOBODY would believe that someone named Clark Kent would DARE take on a Superman persona!
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