Aha, so that's why I sometimes get the question to create a certain column because it is not present in the destination library, when I move ebooks between my libraries.
Until recently I never had paid much attention to the .OPF files and had just vaguely seen that a lot of quote's were used somehow:
Spoiler:
<meta name="calibre:user_metadata:#subtitle" content="{"table": "custom_column_6", "column": "value", "datatype": "text", "is_multiple": null, "kind": "field", "name": "Subtitle", "search_terms": ["#subtitle"], "label": "subtitle", "colnum": 6, "display": {"use_decorations": false, "description": "Subtitle"}, "is_custom": true, "is_category": true, "link_column": "value", "category_sort": "value", "is_csp": false, "is_editable": true, "rec_index": 26, "#value#": null, "#extra#": null, "is_multiple2": {}}"/>
Now that makes sense.
I did found too that I could remove that embedded metadata via the plugin "Modify ePub" whenever that might be needed. So everything is under control.