Hello,
this has changed since your post. PDF to Excel now uses a new converter developed by PDF24 that creates one worksheet per table: a table that continues over several pages ends up in a single worksheet, and the repeated header row is left out. This is the default online (https://tools.pdf24.org/en/pdf-to-excel) and in PDF24 Creator since version 11.31.0. Only with the option "One sheet per page" does each page get a worksheet of its own.
If the pages contain different tables (with different columns), each table still gets its own worksheet. An option to put everything on a single worksheet does not exist yet. Thank you for the suggestion, we will add it to our list.