The scope of paper duplication checking includes the whole paper, not just the text. Because there may be problems such as quotation and plagiarism in all parts of the whole paper, if you only check the text, you may ignore the problems in other parts, resulting in inaccurate test results.
Usually, the paper detection tool will check the whole paper, including the text, references, appendices, footnotes and endnotes. When checking, these tools will compare the paper with other known documents, documents and databases on the network, so as to find possible problems such as citation, plagiarism and so on.