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Yes, in this context the definition of "rebase" is as follows.
To "rebase" is the process of modifying data based on one specific reference to now be based on another different reference without changing its underlying functionality.
In Sigil, you are modifying all opf manifest ids from their previous naming basis (whatever that was) to now be based on their current file names without breaking any functionality.
That means making sure to properly update the spine, update the smil references in metadata, update the cover image metadata, update any bindings, updating manifest fall back properties, and any media-overlay properties just to make sure you do not break the opf.
This tool may be particularly useful after renaming files en masse so that the current manifest ids do not reflect the now changed earlier file name which can cause confusion when examining or hand editing the OPF.
This tool was added based on requests from users to "fix" manifest ids after a file was renamed like Sigil used to do but that old approach was too slow for large renames and unfortunately could result in broken functionality especially under epub3. So that practice was stopped to avoid creating bugs since the spec called for unique ids only.
Over the years people just got used to basing these ids on filenames.
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