I don't see that as being the case. The 'six second rule' was introduced in 2000. The first time the laws included a provision about a player not being allowed to challenge a keeper when they're in control of the ball was in 2007. Conceptually, I don't see them as being particularly closely related. The typical situation where the keeper is being restricted by the six second rule (in as much as they ever are) is when they're standing there with the ball in their hands.
I think the restriction on challenging is more aimed at the situation where the keeper is trying to gather the ball (either on the ground or in the air) and a player is trying to kick or knock the ball out of the keeper's hands. It's especially important to protect the keeper while they're diving at the ball on the ground, to prevent them being kicked in the head (or body, or hands or whatever) but it's also important to protect them while they've got their arms extended above their head which leaves their whole body exposed and vulnerable.
In any event, whatever the reason why the provision was first introduced, I don't think there's any doubt that the actual wording of the law is fulfilled here.
The law says:
In this image, de Gea clearly has the ball between the hands and is clearly being challenged by van Dijk.
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