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After Effects does not use ASS subtitles at all, although there is Shinjipierres script for importing karaoke timing from them. I don't know how that works though... actually I don't know too much about it at all so don't take anything I say for truth.
Aegisub is an ASS subtitle editor. It doesn't actually render anything, but for karaoke there is the Automation system that allows you to generate massive effects.
OverLua is yet another completely separate system. It doesn't have any such thing as a native data format, although it (as far as I know) has only been used with ASS files so far: The idea in OverLua is that you write a program (script) that renders whatever, usually karaoke effect.
The approaches used in the three are widely different.
After Effects is mainly targeted towards direct freeform visual manipulation. It supports some extensive scripting that can eg. automate generating effects for multiple objects.
Generating ASS karaoke is basically generating a kind of rendering list: A list of objects, descriptions of how they look and how they animate. That's what Aegisub's Automation does.
OverLua is direct rendering: You write program code that draws directly onto the video frames. You can use a large number of approaches to actually doing that. ("If you don't already know how to use it, don't bother trying at all.")
I think your question is how to do effects like what can be done using \clip in ASS. You're taking the wrong approach to the problem.
First, pick a tool. Then, knowing the boundaries of what can you can reasonably do with that tool, pick an effect you want to do. Finally, using the appropriate techniques for the tool of your choice, make the effect.
The use of \clip in ASS is a technique, ASS is the tool. You seem to be approaching the problem backwards and thus end up in a corner with no way out.
If you're thinking of doing a specific kind of effect, and you seem to have picked After Effects as your tool, then give a description of what the effect you want to make should look like (or give an example) and then someone can perhaps help you how to approach the problem.
Remember, a description of how an effect looks does not include words like "layer", "clip" or "mask", those are technical implementation-details.
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