Hi there. I thought that this 'bubble' looked familiar, the same exists in my 2017 2.2D, and I believe that it is manufactured in this way to allow space for the fuel rail. The fuel rail sits perfectly into this groove. I also have the same black dot that you mention, must be something related to production tests.
I don't know about the broken legs on the nuts. Perhaps this is just a security seal to prove that the injectors haven't been touched when in dispute over warranty repairs.
Here's some pics from mine.
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