I would use the friendship as a secure base, then gradually widen it.
Constantly separating them from day one can make training feel like adults are taking away the person who makes them comfortable. Keeping them together all the time can make the dependency stronger.
So I’d mix it. Some activities together, some apart. When they are separated, pair them with children who are likely to make the experience positive.
In games, I would not tell them “stop passing to your friend”. Instead help them scan the whole picture: “Who else can you see?”
I’d also praise moments where they connect with another teammate.
The target is not breaking up the friendship. It is helping each child discover they can enjoy football and make decisions with the rest of the group as well.
Good friendships are a strength; dependency is the bit you are gradually reducing.