Honestly, the more I think about this the less it makes sense. My guess--and it's basically just a guess--is that it's just not that hard to slip between the Great Sea that used to be Hyrule and the one in the Realm of the Ocean King. (That, or he actually brought his entire realm to Hyrule at the end of the game.)
These are the people we see travelling between the two realms in PH:
-Link and Tetra
-The Ocean King and the three fairy spirits
-Linebeck
-Beedle (though this is uncommented on and it may just be an alternate Beedle a la Termina. Actually, that throws off my entire theory, as we'll see below.)
But in Spirit Tracks we see descendants of other inhabitants of the Ocean King's Realm:
-Jolene: The operator of the [Something]-Em-All minigame whose name excapes me.
-The mechanic who repairs your crane and swaps out ship parts: The bridge builder.
-Phantoms: Phantoms.
-The mailman: The mailman with a much less ridiculous uniform.
-The Anouki: Possibly the same tribe ("We used to live on an island") but probably descendants.
Though these could easily be Termina-style alternates. (Hey, WW-Link and Tetra used to live on islands, too--doesn't mean they came from the Ocean King's realm.) Which would mean that their appearance has nothing to do with Linebeck in the ending of PH.
Ultimately, whether they're alternates or descendants, I'm chalking Spirit Tracks' recycled character designs up to laziness: There are plenty, many having little to do with alternate realms (e.g. Alfonzo, Link and Zelda, Linebeck, Beedle, and I think I saw Snot Kid.)
Also, I think I just remembered something that may largely invalidate my theory: Didn't the Ocean King say that he and the fairy spirits had to return to their realm? Made it seem kinda permanent. Then again, after what they pulled with Midna, I don't know what to think.
So never mind. Lesson: I should be sleeping right now instead of doing Zelda theory.