If the problem is restated as finding the white input boxes in the pdf (credit to comment from [K J](https://stackoverflow.com/users/10802527/k-j)) it can be solved fairly simply:

import fitz  # PyMuPDF
import csv

INPUT_PDF = "input.pdf"
OUTPUT_PDF = "output.pdf"
OUTPUT_CSV = "output.csv"


def colour_match(color, target_color=(1, 1, 1)):
    """Return True if color exactly matches target_color, else False."""
    return color == target_color


doc = fitz.open(INPUT_PDF)

# Page numbers are zero based
# pages_to_mark = list(range(len(doc)))  # Default filter for all pages
pages_to_mark = [1]  # Example: only process page 2

with open(OUTPUT_CSV, mode="w", newline="", encoding="utf-8") as csvfile:
    csvwriter = csv.writer(csvfile)
    csvwriter.writerow(["page_num", "x0", "y0", "x1", "y1"])
    for page_num in pages_to_mark:
        page = doc[page_num]
        drawings = page.get_drawings()
        shape = page.new_shape()
        for d in drawings:
            rect = d.get("rect")
            fill_color = d.get("fill")
            if rect and colour_match(fill_color, target_color=(1, 1, 1)):
                x0, y0, x1, y1 = rect
                cx, cy = x0, y1  # Lower-left corner for circle
                # Draw circle on PDF page
                shape.draw_circle((cx, cy), 2)  # Radius = 2 points
                # Write full rect coords and page number to CSV
                csvwriter.writerow([page_num, x0, y0, x1, y1])
        shape.finish(color=(0, 0, 1), fill=None)  # Blue stroke circle, no fill
        shape.commit()

doc.save(OUTPUT_PDF)
doc.close()

The following image demonstrates the solution by showing character boxes on page 2 which were not previously returned: