I've seen those takes and don't disagree. But I feel that scene is pointing out that this group of scouts have wildly different and completely contradictory analysis of the same player, and the girlfriend angle is supposed to demonstrate the absurdity of some of that analysis.
Your first paragraph is a good point, but all it does is point out another weakness of the scene. The "ugly girlfriend" thing is funny, but how representative is it of how professional baseball scouts judge prospects and potential signings? Is it a scarecrow? Yes, good baseball people can disagree about a player in good faith and for a good set of reasons, but how often were those reasons so silly, particularly when the demonstrated track record of the A's front office staff was so obviously strong?
When the lead scout senses Brad Pitt is mad and decides to get a little more serious, he says, "Look, we’re gonna find 25 guys, put ‘em through player development, teach ‘em how to play Oakland A's baseball."
That is exactly what they did to put together such a good roster in the first place. They scouted and developed well. Why is Brad Pitt so mad the plan is to do it again when it handed him Hudson, Mulder, and Zito?
I've read that both the book and movie took a lot of liberties with the actual facts so who knows if a conversation like that actually took place. I know that the starting pitching staff, which was barely discussed in the movie, was amazing for that team and a big reason for their success.
This site here --
https://bleacherreport.com/articles/1045951-25-most-impressive-starting-rotations-in-mlb-history#:~:text=1.,1998 Atlanta Braves&text=And, finally, the greatest pitching,with 16 or more wins.
...has the 2002 A's with the 22nd best pitching staff of all-time.
That defined the team's success, not the few buy-low position players they found on the scrap heap to fill out the lineup.
For context, that article puts the 1998 Braves as #1 all-time, which with a rotation of Greg Maddux, Tom Glavine, Denny Neagle, Kevin Millwood, and John Smoltz. That is almost a self-evident choice.