Content dependencies are also soft dependencies. This missing that if they are missing then the configuration should not remove them if resaved. This means that if the content does not exist during configuration import and the config entity is created the content dependency should not be removed. For example, Block content blocks lose their dependencies when exported after being imported before the block content entity existed.
If I have a module that provides some block placements and default content for the block entities themselves, the block placements are imported first and then the block content. This is allowed because of the fallback plugin for blocks. If you immediately attempt to re-export the block placements, the dependencies will be lost.
Don't clear out content dependencies when recalculating configuration dependencies.
Discuss approach, review patch, add tests.
User interface changes
Data model changes