Yes, Liston did give Ali a few problems, at least early and of course when Ali’s vision was impaired. I think it was in answer to Ali’s unmarked face and the apparent ease of his Miami victory when Dundee noted that Ali had multiple welts on his body after the fight - indicating the less visually apparent damage Liston had caused. That body shot…that’s the one announcer Steve Ellis reacted to saying “Ooh, a hard, heavy shot dug under the heart” - or words to that effect - That punch was notably audible - a huge punch but it just so happened to be received by an opponent who would go on to become a legend for taking such punishment to the body.
Ali's prime is a complex subject. Yes he was better than when he finally showed himself to be human, but his opposition was significantly weaker. Now great as Ali was, I don't think that he was greater than the entirety of heavyweight history, that came before him. There is someone who could take his 0 in that mix, we just have no idea who it was. That is quite a compliment.
Louis is the only who would be favored but Tunneys got a good chance. I like Braddocks and John Henry Lewis's chances at their peak potential. I'll throw Wills and Farr in there too. Ali is too durable for me to pick Dempsey, Baer or Fulton. Their chances really rest on getting Ali down and Ali went through his entire championship career getting knocked down twice. All three would also struggle with a fighter that large that good. Dempsey faced boxers on Alis level and he fought guys bigger than him he never fought both in 1 package. Baer and Fulton fought Louis and Wills. This also depends on the roundage. If we've got a 6, 8 or even 10 rounder the amount of fighters who are capable of beating Ali is much greater. Thats where a lot of those smaller P4P greats have a shot.
Of the Pre Ali Heavyweights, Joe Louis is the one who could have beaten Muhammad Ali most times. I believe Jack Dempsey, Jack Johnson, and Rocky Marciano could have picked up a win or two in a best of seven fight series with Muhammad Ali.