I suppose that if you don’t think about it much, it may sound like higher praise, analogous to putting artistry above craftsmanship. It’s probably meant admiringly, while also—as you suggested—excusing someone else’s (the speaker’s?) inferior performance by implicitly blaming lack of an inborn magical ingredient.
In my opinion, raw talent isn’t worth much by itself; it has to be developed with a lot of work—training, discipline, and guidance. The results are also easily confused (by others) with passion, dedication, and grueling practice. Maybe the talent is a gift for loving something enough to be devoted to mastering it without burning out.
I like Malcolm Gladwell’s collections of anecdotes, even though I don’t regard them as science; and Outliers does a good job of showing what it takes to turn so-called talent into success.
Some talents may be inherited; but on the other hand, what may be happening is that those young people are growing up in an environment that places an extremely high value on the art, music, athleticism, or whatever of the parents, and so those skills are well cultivated. I don’t think you can simply decide to have a great operatic voice; but can you learn to hit a ball? I think so.