If we allow data files to travel in the epub container for use by scripts without having to meet CMT requirements, shouldn't we also allow foreign data in script tags?

It's not completely clear to me if it's allowed, as it depends on how you interpret "embedding" here:

it is not embedded directly in EPUB content documents (e.g., via [html] embedded content and [svg] image and foreignObject elements).

Since it's not a definitive list of cases, and the data is embedded in a content document when in script tags, that seems to make it illegal. But it doesn't make a lot of sense to allow in external files but not in script tags.