Ali actually was huge at the time. He was 205 and 21 years old when he fought and got decked by a 185 lb domestic level fighter in, Henry Cooper. The fight before that Ali went the distance with 188 lb journeyman, Doug Jones. So no, I don't think there's anything wrong with a 39 year old Wlad losing 3 rounds to a top 10 contender who is 9 years his Junior and displayed solid defensive skills. When Ali was 39 he was getting beaten by Berbick and Spinks. Now I believe Ali is the greater of the 2, but just appreciate Wlad, he's great in any era.
If you don't believe Ali was big here are the weight and height advantages/disadvantages for every one of his fights from the Archie Moore fight on. Moore: +13 lbs, +4inches Jones: +14 lbs, +3inches Cooper I: +17 lbs, +4.5inches Liston I: -8lbs, +2 inches Liston II: -9lbs, +2inches Patterson I: +17 lbs, +3inches Chuvalo I: -2lbs, +3inches Cooper II: +13 lbs, +4.5 inches (this was the lightest Ali would weigh for the rest of his career) London: +9lbs, +3inches Mildenberger: +9lbs, +2 inches Williams: +2lbs, 0 inches Folley: +10lbs, +2 inches Quarrey I: +16 lbs, +3inches Bonavena: +10 lbs, +5inches Frazier I: +10 lbs, +4.5 inches Ellis: +30 lbs, +2 inches Matthis: -25 lbs, -3 inches (Mathis was a GIANT of the era and ended up walking around at 500+ lbs later in life) Blin: +22 lbs, +2 inches Foster: +15 lbs, +2 inches Chuvalo II: -5lbs, +3inches Bugner I: -6 lbs, -1inch Quarry II: +18lbs, +3 inches Patterson II: +30lbs, +3inches Foster: +40lbs, 0inches Norton I: +12 lbs, 0 inches Norton II: +7lbs, 0 inches Lubbers: +21 lbs +3inches Frazier II: +3lbs, +4.5 inches Foreman: -4 lbs, 0inches Wepner: -2lbs, -2inches Lyle: +5lbs, 0 inches Bugner II: -6lbs, -1 inch Frazier III: +9lbs, +4.5 inches Coopman:+20 lbs, +4.5 inches Young: +21 lbs, +1 inch Dunn: +15lbs, 0 inches Norton III: +5lbs, 0 inches Evangelista: +15lbs, +2 inches Shavers: +14 lbs, +3inches Spinks I: +27lbs, +2inches Spinks II: +20lbs, +2 inches Holmes: +6lbs, -1 inches Berbick: +20lbs, +1inches So, Ali had on average a 10.3 lb weight advantage and a 1.8 inch height advantage. Go back through Wladimir's history, back to when he was weighing in closer to 220 lbs and do the same thing. You will notice that he and Ali are almost exactly similarly large for the division given the time period. Size is a part of boxing, it's one of the 'gifts' that people like to talk about. Both Ali and Wlad were gifted with size and then were lucky enough to also have tremendous reflexes and speed of hand and foot for that size. Ali liked to clinch too btw
Head to head, prime for prime I believe Wlad holds a number of physical advantages over Vitali, including hand speed and foot speed, power, and better technique. I believe Vitali has better timing, is a more fluid puncher, clearly has a better chin and better stamina than Wlad. The clinching Ruiz-esque Wlad that we now see is often compared to the iron chinned, go out on his shield Vitali which was only really seen vs. Lennox. When making comparisons, they should both be considered at the heights of their respective skillsets.