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The issue is so few epub3 readers support javascript (support for scripting is not a requirement for epub3 compliance), and even fewer epub3 epubs use it, especially commercial ones. So I doubt there is truly much of a need.
Why don't up you instead use a Find/Replace Saved Search to remove your standard js insertions and a create a Clip specific to each to insert them easily. That way insertion and removal can become quite fast.
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