The appearance handling for forms in 1.x is limited and does not reflect all settings possible for form fields. In addition the current code is not very modular and does not follow the box model used for form fields.
Unfortunately only the basics of form handling are defined in the PDF spec. The details like padding of boxes, text placement etc. have to be determined by looking at how Adobe forms are generated.
Update: The file from
PDFBOX-2310 has bad rendering which might be related?