A number of reasons.
What Everton do in training are different from what most clubs do. What Evertons players do in matches are different from what players from more offensive minded teams told to do.
McAtee have learned his trade in a club where you react by running towards the ball when your team give it away, while at Everton you run away from the ball to find your place in a low block. It's a totally different mindset.
There will be plenty of fullbacks in the league next season that have much more offensive positioning than Everton's wingers. 60% of your game will be defending and tracking runs deep into our defensive half. It is very rare in modern football to see offensive players be asked to play so deep.
Look at Bournemouth. Do you think it is completely random that their players are so attractive for big clubs? Do you think it's caused by good recruitment or the fact that Bournemouth has a style of play that is liked by analysts, scouts and managers throughout Europe? Sporting directors and managers see players do things that could be useful for their teams. It's all on the manager. And while results haven't been fantastic, he has added so much value to the club. And made Bournemouth very attractive for young players.
It is easy be impressed by Branthwaite putting himself on the line and defend great in Everton's low block. But that isn't useful for teams defending that low twice a season. There are thousands of central defenders that can look impressing in a low block.
If you look outside England, where club's can't rely on tv money and developing talent to sell on with profit is a necessity, teams have understood that to make money they need to mirror the tactics and style of richer clubs. Because that is their market.
For McAtee to do well for Everton, he'll need to unlearn much of what he has learned at City.