All signs point to Marvel owing the rights. During the late 1960's, Marvel staged a brief revival of the character in Fantastic 4 Annual #4, allegedly to prevent the creator (Carlos Burgos) from regaining the copyright, indicating that they at least valued it slightly.
In fact, Burgos’s claims may have never made it to court; his dark
ritual on that summer day may have instead been reaction to a new
Marvel comic book. In early August, Lee and Kirby’s Fantastic Four
Annual #4 featured Burgos’s original Human Torch, battling the new
teenage Human Torch and the rest of the Fantastic Four. Cover-dated
October 1968, it appeared exactly twenty-eight years after Marvel
Comics #1-in other words, exactly as the initial twenty-eight-year
copyright was expiring. The original Torch had been revived just long
enough to ensure their copyright claim-only to be killed again, pages
later. “Well, let’s face it,” mused the Thing when Burgos’s creation
had been extinguished, “ya win a few . . .’n ya lose a few!” Lee had
Johnny Storm, the last Human Torch standing, eulogizing his fallen
predecessor this way: “He tried to defeat me . . . and yet, I can’t
find it in my heart to hate him!”
When Carl Burgos tried to sue for the Human Torch
More recently (in 2014) the Human Torch android was featured in All New Invaders, presumably to prevent the image and naming rights from reverting to the creator's estate and possibly coming into conflict with the existing (and more popular) Johnny Storm 'Human Torch'.
For the record, the fact that they're the rights-holder doesn't necessarily mean that Marvel haven't come to an agreement with Fox over the use of the name "Human Torch", just that such agreements are usually shrouded in secrecy. Even if the law favoured them, it seems unlikely that Marvel would risk a multi-million dollar lawsuit (and potentially an injunction against a $100m+ film) just to spite a competitor.