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Layer styles has never been fully integrated in after effects.
If Layer styles was moved into Effects, you could use it with the other effects in the order you want.
There are no "after effects logic" in the way Layer styles is integraded right now.
Honest answer: Probably too big of an elephant to fix now after so many years. Photoshop itself is struggling with handling their "flexible layer styles" (multiple instances of the same effect, reordering etc.) they introduced two years ago and unless this gets sorted out, I don't see how this would be possible to do in AE, either. Perhaps this can be implemented once the Properties Panel sees the light of day and layer styles can be managed there instead of clunkily on the timeline, but this is probably as good as it gets. I would not expect this to ever be turned into actual effects as ultimately there are soem advantages to having them the way they are now.
Since After Effects Layer Styles are part of the Photoshop to After Effects workflow, they should remain where they are.
If anything, After Effects Layer Styles could be updated to match how they have been updated in Photoshop (namely being able to stack instances of Stroke, Inner Shadow, Color Overlay, Gradient Overlay, and Drop Shadow), full support for Blend If (not just On/Off), and a method of reloading current settings from the Photoshop source. Hmmm... sounds like I have a feature request to post.