I agree, this looks like a regression bug. You may want to report it; but since it has a workaround, namely using cli-diff-delete-before in the container B, I would not expect the bug will be addressed quickly.
Can you change those annotations? It’s not a backward incompatible change if you do so.
A good practice is to always keep annotations outside of the main module, by creating an “annotation” module. You may already be doing this, or maybe not. But it’s a good practice to keep in mind, as the potential annotation changes can be isolated in one module.