PDF Text Extraction Order Not Matching Visual Layout Despite Correct Coordinates

Question

I am working on extracting text from a PDF using PyMuPDF. However, I am encountering an issue where the extracted text order does not match the visual flow/Layout flow of the PDF.

Details of the Issue:

1. The PDF's text is correctly positioned according to its coordinates (bounding boxes), but the logical extraction order is incorrect.
2. For example, on the first page of my PDF:
   • After extracting line 2, the tool directly jumps to a table at the bottom of the page, skipping intervening text.
   • Later, it picks up lines 3–20 in an unordered manner.
3. I have verified that the issue is not related to column or layout misalignment, as the coordinates are accurate.

What I Have Tried:

• I previously posted similar questions here, and the suggested approaches included:
• Sorting the extracted text by y (vertical) and x (horizontal) coordinates. Using tools like PyPDF2, PDFMiner, and Adobe Acrobat for re-tagging.
• However, these approaches did not solve the issue, as the extraction tools seem to rely on the internal encoding order of the text objects, which is inherently flawed in my PDF text output.

Additional Information::

• I am not looking to perform OCR, as the text is already present in the PDF.
• The document contains multi-column layouts and mixed elements like tables and have complex layouts in the PDF.