I've gotten clarification on the matter, and it finally makes sense. Apparently the determining factor isn't whether or not the player is on his entry-level contract, it's whether or not the player is an entry-level player (in the first three years as a pro, with the clock apparently starting to run once the player is Calder Trophy-ineligible for the following season).
How this plays out is that Alex Semin is in his fourth year as a pro - his rookie year in 2003-04, and two years in Russia prior to returning to the NHL this year. Kari Lehtonen (in his second year, by this definition) and Peter Budaj (also in his second year), on the other hand, are eligible for the YoungStars, despite being, like Semin, not still in their respective entry-level contracts.
No conspiracy, no waivers... just rules.