The thing is, what is a perfect guitar for the factory doesn’t necessarily make it be perfect for you, me, or the rest of the people who play it. Right out of the box it needs to talk to you, to sing to you.
My Taylor acoustic was found after auditioning six others of that model, including pulling unplayed ones from their unopened shipping cartons from the store’s back room, and she was in the last one that the store had. I hit a chord and knew immediately. She sings.
Every one of my guitars has been reworked/adjusted in some way or another except one, my PRS 509. And even that one got there by a circuitous route. I bought it used, and the neck pickup wasn’t at the right height according to the PRS specs, assumedly because the former owner adjusted it to their taste. While raising it one of the coil wires pulled out of the pickup. PRS doesn’t sell them for repairs anywhere else but at the factory, so I shipped it back and while it was there had them do a full setup on it because I was curious exactly how the factory would do it. It came home and it actually is perfectly set up, for me and I haven’t felt a desire to change it.
A lot of companies have a specification that puts the strings too high or the pickups too low and we have to use experience and knowledge to know what it should be. That information is usually easily found on the internet.
It also helps a lot to have a really good guitar tech nearby who knows how you like your guitars to be setup and who happily will put down whatever they are working on to inspect it and give their opinion, and then wonder out loud why TF you bought THAT when you already have other great guitars, and when you thank them for their review and reach for it to stick it back in the case they hold it back and begin adjusting it to fit you just right. Good quality guitars should already be in the ballpark for what is acceptable so it takes a little bit of adjustment to make them great, and the tech is done in a minute or two.