So you asked why would you actually describe the formation as a 4-2-3-1 if De Jong started in defence every time they had the ball?
The answer is 4-2-3-1 doesn't mean it's 4-2-3-1 when on the ball, it could also be 4-2-3-1 in defensive transition but different shape when on the ball. For example 4-2-3-1 could look like 3-4-3 if the full back are pushed forward when they had the ball or 4-3-3 could also look like 3-2-4-1 when they had the ball. Lot of variety.
FDJ received free role where he can drop to the defensive line or stay in midfield next to FDJ or drive/dribble the ball from deep defense area to midfield area, he's basically roaming in different places and this is why you want the deep-lying midfielder played next to FDJ who was given the modern libero role if we play like the Ajax 18/19 season.
Pictures below show Schone position is deeper than the full backs means he's not really box to box or someone who gets license to go forward but his role is more deep-lying midfielder while FDJ was deeper than Blind (he played the modern libero role).
Pictures below show Schone position is on the similar line as FDJ but the full backs are higher than Schone means, again, it shows Schone role was more a deep-lying midfielder.