If the PDF to be appended is generated from FileMaker by a Save As PDF script step, yes this is possible.
A script could:
1) Use export field contents to export the current copy of the PDF to the temporary items folder
2) Use Save as PDF with the Append option to append additional pages to the PDF document.
3) Re-inserts this modified copy back into the container field.
All three steps become possible when you use a Variable to compute the path to the copy exported to the temporary items folder.
This could also be done with a "by reference" PDF file, but the steps would be a bit different as you would not have to export and re-insert the file.