Based on this metric, I think Sacchi's Milan comes out on top of the club sides, especially if the imagined matches were played under a variety of conditions.
Well do they ?
In our timeline Sacchi's Milan finished with a single league title and 2 champions league titles. I could see the argument for them winning in 1991 but the 1989 and 1990 wins become more uncertain as they struggled in a penalty shoutout against the red star, and could only advance due to the away goal rules against Bayern, their tie against Malines went to extra time, these are all games that at any moment could go eitherway. So it is not certain that they win the Back to back CL in all of the simulations.
They also only won a single league title, in 1989 they weren't even in the title race so i don't think they ever win that one, 1990 is one that they could take away from Napoli if we were to rerun the simiulation, but in 1991 Sampdoria had a comfortable lead.
So they could win all between 1-2 league titles and 0-3 Champions league depending on the amount of luck that they have.
For Barça, they won 2 league titles comfortably in 2009 and 2011, in 2010 Madrid gave them a run for their money, so i could eventually see that in some instances Madrid could walk away with the trophy even if it's unlikely, and in 2012 i would apply the same reasoning but the other way around. It would be unlikely for Barça to win the league that year but not impossible if certain things go right.
So it seems like 3 league titles is about fair for that team on average luck.
As for the Champions league, i could see the 2009 tie against Chelsea go eitherway (assuming they go past Liverpool considering that tie itself was pretty close), so its not a certainty that they win it in the majority of time.
In 2010, i actually see them going past Inter more often than not, once you consider how much bad luck they had against them. First is that icelandic volcano that prevented all flights in Europe from taking off, which made the team go on an exhausting 20 hours bus ride to play in Milan. There were mistakes made by the referree that put them into a disadvantage like the third goal which was offside and a missed penalty on Alves. So i can see them winning more often than not or at least it's a 50/50.
In 2011 they didn't struggle much to lift the trophy so i think they win in the vast majority of scenarios.
Finally in 2012, i think that out of a 100 times they go past that Chelsea team in 99% of instances, we hit the post like 5 times during the two tie, miss a penalty and waste an insane amount of chances either due to bad luck or an incredible Petr Cech.
So all in all, you could say that Barça finishes with at worst 2 league titles and a single champions league or at best with 3-4 league titles and 4 Champions league if luck is maxed out. Their floor and their ceiling are both higher to the one of the Milan team.
Of course this is all speculation, but it's interesting nonetheless to ask ourselves what could have happened if conditions were different.
I think for peak sides, that Milan juggernaut just has a perfect balance and would be ideal suited to defeating Pep's tiki-taka at its peak. Milan could play either possession, counter-attack, or direct attack. Milan of that era was tested against a higher quality of teams than La Liga of Barca's peak which almost lost to Arsenal in 10-11.
I don't think that we should ask ourselves the question to who would win a potential game between the two because these kind of mental experiments will always favor the modern team because they will have a lot more tactical knowledge access to better training, better medecine...
A lot of tactics that the Sacchi team used for exemple were either outdated (like the agressive offside trap) or something that Barcelona is used to face on a weekly basis (like the famous Milan press which was revolutionnary at the time but is democratized by today).
This. Certainly the 2 best i have witnessed (watching since 1996).
Those two teams are in my opinion the most dominant in history. Cannibalized both their domestic leagues and Europe, and this is also supported by empirical evidence. Found a ranking using the elo method to determin which team is the best in history, Pep Barca and Heynckes Bayern ranked respectively 1 and 2.