Margin Notes can be thought of as on-the-page "story notes."  This means the reader gives their feedback on the script's beats, scenes, characters, the plot, etc. as they read through it.
A Line Edit can be thought of as a "red pen edit." This means it is a dialogue and description edit only in which the consultant tightens both up by adding strikethroughs and rearranging sentences.
In short, a Line Edit doesn't include story notes, while Margin Notes don't include dialogue and description edits.
For more information you can find samples of both services on their respective pages:
Margin Notes
Line Edit
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