I don't know. Ask Shapiro why he loves Atkins.
Just saying what I think is more likely.
The pros for Atkins are sort of obvious. He's generally good at certain things, and probably a middle of the pack GM at worst. Gets value in trades more often than not, makes good free agent signings more often than not. Avoided extending the trap prospect Vladimir Guerrero Jr. (saved the franchise let's be honest).
Almost everything they do at the MLB level in terms of transactions is fine, sensible, and good (despite a lot of belly-aching around here about "not fixing the offense" in one offseason or whatever).
I am envisioning a co-GM scenario where Atkins still has most of the day to day control over the MLB roster. He is the one on the phone, making trades, negotiating with free agents, talking extensions. And then his co-GM is the one who focuses more on drafting and development and more on the statistical side of things - how to do advanced game prep better, communicate information to players and coaches better, and so forth (the stuff Atkins may be bad at).