There could be exceptions, eg. when the user chooses to update links in a Calc spreadsheet, otherwise it's a bug.
Having a list of exceptions could be helpful for reference.
Originally this meta was only about file opening, but there are other situations where document modified status isn't correct.
To check if a document is considered modified, see if the Save toolbar button has the changed marker, or close the file, and see if it asks to save unsaved changes (and whether there should be unsaved changes).