The problem arises since obsidian internally converts the YAML frontmatter into a JSON object. Whenever you make changes to the frontmatter through the obsidian API (properties editor, new bases feature, or any plugin that uses the obsidian API to handle the frontmatter), processFrontmatter is called to convert the JSON frontmatter object back into YAML. Through this conversion process, the original YAML frontmatter format is lost, since JSON doesn‘t support different styles of list definitions as YAML does nor does it support comments.
So the problems you describe are mostly inevitable by the design choice of the obsidian team to handle the frontmatter internally as a JSON object. Technically, it would probably be possible to store additionally hidden metadata fields for list style, comment, etc., so that the original YAML structure could be restored. But since there aren’t even signs that we could get support for nested YAML natively in the properties editor, it‘s even more unlikely in my eyes that we will see support from the obsidian team for this list of list JSON-YAML conversion problem.
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