sort of, at the time Jefferies was not expected to make a comeback and indeed only did so six years later, so hart was viewed as the champion. the question becomes how long after a fighter retires does he lose any claim to the lineage when he returns. theoretically if Lennox Lewis made a comeback today Wladimir Klitschko would still be viewed as a lineal champ by most people. however short retirements seem not to count like during Ali's two year retirement Norton won the vacant title but isn't recognized as a lineal champion. so exactly where you draw the line has never really been decided. so..... sort of
It wasn't perfect, but it is probably easier to roll with it, than it is to squeeze the toothpaste back into the tube.
Hart v Root was a much more proper matchup to name Jeffries replacement than Maher v O Donnell was to name Corbetts. But if it wasn't Hart also had the Jack Johnson win before fighting Root which is what elevated him above all other alternatives. To the extent Hart v Root was arbitrary Root could have been swapped out for a few other people like Gardner, Schreck or O Brien. Hart was always going to be in that fight because he'd beaten Johnson. The attempts to name an alternative champion in the US came after Tommy Burns took Harts belt. One of these was Hart fighting Schreck(who had a win over Burns) and the other title was won by Jack Twin Sullivan(who had beaten Burns for the MW title in Burns previous fight). Al Kaufman would beat both Schreck and Twin Sullivan and would be referred to as the "near champion" in newspapers until Jack Johnson beat him in 1909. That was the more disputed title. This might have been because Hart lost his belt via decision and it wasn't widely agreed that that was a thing yet. But Burns was also a MW non champ who'd never fouight at HW. So there was a lot more basis to challenge Burns title. Hart had beaten Johnson and to this point was undefeated at HW(5-0-2) even if all those fights were close. Most of the criticism of Hart at HW comes from after he lost his title. If not for 3 DQs in fights he would have otherwise lost Harts career would have ended on a 7 fight losing streak. The British NSC did name an alternative champ during Harts short reign but its likely the British were always going to dispute the title when Jeffries was gone and that was less about Harts legitamacy. Hindsight being 20/20 I'd have picked Root to fight Schreck for the title. Root dropping a superheavyweight while weighing 170 pounds in his last fight leads me to think he had a higher ceiling at HW and while Hart beat Root fair and square I think Root winning would have been better for the sport and he had more to give. But as noted at the top of the post Hart was always going to fight for the title because he'd beaten Johnson.