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I'm afraid you can't have it any other way. Somewhere there must be a flat 2D step to apply the effects, so if you use CT in 3D, that indeed can mean building a 3 level nesting hierarchy just to get it. It's sure annoying, but with internally generated items such as text and shape layers it's IMO not that big a problem. Since they can be up-rezed infinitely and still render pretty fast, using huge-ish 2D pre-comps for them is probably an acceptable compromise....
Thank you for your reply!
I was afraid that the answer would be what you stated. It sure would be great to have some way of manually changing the render order for effects in AE, maybe I should make a feature request about it. I have heard many pros asking for nodes in AE, and if I understand correctly, that could be one solution for these kind of issues right?
In the meanwhile, does anyone have a script that would automatically create the required precomp hierarchy for a 3D layer so that these kind of effects could be achieved more easily?
I recommend you check AEnhancers again. I can't point to anything specific, but surely this would be quick to do. The good old Precomp To Layer Duration for instance should be easy to modify to include a second level and then set some of the layer switches to enabled. I'm not sure about the CR switch, but the 3D switch definitley can be set in scripts.