For complex situations, I work a lot with PreComps that I prerender to make a final composite.
How great would it be when Ae could help in a modern way to manage this.
I think of adding a 'Freeze' switch to each layer, as already kind of exists for RotoScoped footage layers..
Another great example of this workflow it how Logic Pro does this: simple click a freeze button, and the track / layer is rendered. Unfreeze brings it back to an editable version.
This would streamline these kind of workflows, without a lot of hazzle.