I have many PDF files created with SAS ODS Software and have to convert them into Excel Format (*.xlsx). With Acrobat X and „File – Save As – Spreadsheet – Microsoft Excel Workbook“ this worked fine. But with Acrobat XI this works only if the PDF has ONE PAGE only, otherwise the headlines/titles of the PDF are missing in the Excel-file.
It is what it is. In part the problem you describe stems from the quality of the PDF created from the specified software.
PDF, in and of itself, has no concept of tables, rows, columns, "styling", etc.
Expect to have to do post-processing cleanup with Excel.