Simple repro:
pandoc -f markdown -t docx -o test.docx --filter=pandoc-docx-pagebreakpy README.md
Outputs Page Break
pandoc -f markdown -t html -o - --filter=pandoc-docx-pagebreakpy README.md | pandoc -f html -t docx -o test.docx --filter=pandoc-docx-pagebreakpy
No output