Remove Story panel, make optical alignment a paragraph attribute.
The Story panel has only one option, optical alignment, and it is badly implemented. It applies to an entire story across multiple text frames, columns, and pages, and has one value for point size regardless of the point size of the various styles used throughout the story.
Instead, make optical alignment and hanging punctuation two paragraph attributes. Allow the point size to be left black, forcing InDesign to apply the current size for each paragraph.