Do I understand correctly that you used this tool for example for "ug-cs_x-road_6_central_server_user_guide.md"? To be honest I would prefer if headers would contain numbers ("1.2 References" instead of "References" in TOC). But if this tool can produce only bulleted lists then it would be really bad to have both bulleted and numbered list at the same time. Did you remove numbers manually, or this tool did that?
Tools, at least markdown-toc, don't not do anything for numbering. If there are numbers in the headers, they remain int the toc, if not the toc will be generated without numbers.
Do I understand correctly that you used this tool for example for "ug-cs_x-road_6_central_server_user_guide.md"? To be honest I would prefer if headers would contain numbers ("1.2 References" instead of "References" in TOC). But if this tool can produce only bulleted lists then it would be really bad to have both bulleted and numbered list at the same time. Did you remove numbers manually, or this tool did that?