Well, some effects does only work inside the boundaries of the layer so the only way to make it work is to precompose your layers before applying the effect. For this kind of distortion I recommend you to use the CC Bend It Effect under the Distort category. This way you can tell AE where to start and finish the deformation and have more control about it without precomposing.
As Jose already pointed out, most effects will default to working within the layer bounds and with shape layers that's always the comp size, not the visible content of the layer. You need to adapt your workflow accordingly.