All of these have to do with the rigid order of rendering. First this, than that.. Always.
In some cases it would be better to change that order to achieve a result more comfortable.
(Compare how this works in most 3D applications)
Wouldn't it be great when the user can decide the render order (per layer)?
Effects first, then Layer Styles. Or Layer Styles first, then Effect.
And 3D-Transform first, then Rasterize or vice versa.
I think this is rather fundamental to AE's architecture.
But maybe a solution, meanwhile, would be to let AE do an 'internal PreComp' for us,
when we click a (new) Layer checkbox called: 'Handle as if Pre-Composed'.
This should After Effect have to handle the layer as if it were a Composition, without having the user to make Pre-Compositions for every Layer that needs it.
The benefits may be clear: Faster working, less compositions, easier versioning of complex graphics (without having several Pre-Comps per version), less confusing projects