Do not be shy to hack away and change them so the conversion fits expected goals. These files are there for a reason - so the user can view them and modify them according to specific needs. Note: The converter includes a configurables/ folder that contains all data files with rules it uses during conversion. For more information feel free to ask for clarifications on forums or take a peek at the code. Here is a general list of Converter capabilities and conversion mechanic explanations.
1.11 Cores, States, Territories and Colonies.1.5.2 Cultural and Religions conversion in EU4.