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Documenting this bug here, uncovered while working on the following:
It seems that changing opacity via keyframe animation causes a strange rendering bug in Chrome for Android 4.0.x (Ice Cream Sandwich) only, wherein the overlay appears to be rendered above the popup, but the popup remains interactable as usual—the same behavior displayed in the issues linked above. While this issue is not present outside of Chrome for Android 4.0.x, the fade animation did cause a visible lag on many underpowered devices—as such, at least for the time being, the default fade has been removed.