The issue with the way you're looking at things is you're valuing age over actual accomplishments and level. Guys like Werdum in 2006, Cro Cop in 2003 Sergei in 2004 and Herring in 2002 are good wins, but these guys weren't accomplished HWs at the time, they barely had any top wins and were green. The only one that was a established top HW was Barnett. You're taking what these guys accomplished later in their careers when they developed and going back in time equatting them to the same level. Just cause Werdum beat Fedor and was UFC champ, doesn't mean beating him in 2006 is a great win.
Stipe's oppoents were older, but at that time they were on top of their game. Werdum was on the highest point of his career and champion, DC same thing, JDS and Reem were tilte fights. Beating Werdum at 38 when he's champ and at the highest point, is more valuable than beating him in 2006 when he was 2008 and barely had any top wins. All of Stipe's wins were over opponents that were far more developed and a higher level.
You contradict yourself by valuing those wins so high and then devaluing a win like Ngannou. You mentioned Ngannou was Green, despite having 6 UFC wins including wins over Overeem, Blaydes and Arlovski which is more than what all of those guys did at the time. And then mention he lost to Lewis after. Well, after Nog beat those guys, Cro Cop got KO'd by Randleman, Herring lost multiple fights and the other didn't do much for years. At least Ngannou put together a streak and won the belt.
I don't see how anyone can rank DC over Stipe considering Stipe is 2-1 H2H, more title defenses and stronger wins overall. Same with Werdum.
The other reason why I rank Stipe high is because of his accomplishments and how they are relevant to the current time in mma. Today its about top wins, title defenses and big legacy fights. Back then it was winning streaks, more volume of wins, fighting in different promotions. Stipe is more in line with today and what is valued. But that's just my personal assessment.