import fitz

src = r"c:\wamp64\www\AnnexesGU\PG1-A025.pdf"
ref = r"c:\wamp64\www\AnnexesGU\PG1-A025 revisee.pdf"
out = r"c:\wamp64\www\AnnexesGU\test_overlay.pdf"

rect1 = fitz.Rect(14.2, 588.7, 14.2 + 184, 588.7 + 222.8)
rect2 = fitz.Rect(198, 688.7, 198 + 377.1, 688.7 + 136.4)

doc = fitz.open(src)
doc_ref = fitz.open(ref)

page = doc[0]

page.add_redact_annot(rect1)
page.add_redact_annot(rect2)
page.apply_redactions(images=fitz.PDF_REDACT_IMAGE_REMOVE)

page.show_pdf_page(rect1, doc_ref, 0, clip=rect1)
page.show_pdf_page(rect2, doc_ref, 0, clip=rect2)

doc.save(out)
doc.close()
doc_ref.close()
print("Success")