I will give you my reasoning.
The biggest factor for me is that Stipe was the #1 HW from 2010 to 2020 decode. There were several great HW's , but considering wins, record and title defenses, Stipe was the top guy. The UFC was the premier and top organization by far in MMA that decade. And he is the UFC HW goat. So considering those two things, I think it's fair to put Stipe #2 all time. I can't have the best HW of the last 10-12 years, which is a substantial time in mma, not be #2.
The other is that Stipe is the most accomplished MMA HW champion. Most defenses and title wins.
Stipe beat guys at their best and in title fights and that's what counts. The fact that Werdum was 38 is not relevant, he was HW champion. Beating Cormier 2x in his late 30s and early 40s counts big time, Cormier was HW champion. Same with JDS and Reem, these were all HW title fights. Those wins count for more than beating Cro Cop, Werdum and Sergei at the time Nog beat them. So Stipe's wins hold more value beause they were title fights vs the top proven opponents.
Stipe wasn't the best HW from 2010-2020. He became champion in 2016.
Also he didn't beat anyone at their best.
Werdum went 4-5 after Stipe beat him
JDS went 1-5 after Stipe beat him.
Overeem had been knocked out in the UFC 3x before Stipe fought him.
Arlovski was 37 and had been knocked out many times before he fought Stipe.
Ngannou lost his very next fight to Derrick Lewis after losing to Stipe. That's not someone who's "at their best"
Cormier was 40 coming off back surgery and never fought or won another fight again.
Don't get me wrong these are good wins but:
it's not as good as Nog beating Mirko when he was ranked #3 and in his 20s who went on to win a Pride GP.
It's not as good as Nog beating Barnett who was ranked #3 and in his 20s and went on a 10 fight win streak after losing to Nog.
It's not as good as beating Werdum when he was ranked #7 and in his 20s and went on to beat Fedor and then later Cain to become the UFC HW champion.
It's not as good as beating Sergei when he was ranked #5 in the world and in his 20s. A guy who went on to beat much better younger versions of Reem and AA.
Or Heath Herring who was ranked #3 in the world and in his 20s.
For me it's not even up for debate. If it wasn't for Nogs losses to Fedor the GOAT his record would be 32-1 in his first 33 fights while fighting the best HWs on the planet while they were in their 20s and at their best.
Stipe is still a top 5 HW all time and an all time great who is worthy of respect but he's never beaten an all time great HW in their prime. Lost to the youngest versions of the all time greats that he fought.
Retired with less fights and lost to Struve 10 fights into his career as a 30 year old. Something that wouldn't have happened to Nog.
Minotauro undisputed #2 HW of all time.