I want to keep this.  The reason for these lines is that you can have a manual.pot file that you have filled manually and that you are merging those to the main pot file.  But those message ids may already be in the main pot file because someone has improved the i18n usage in the code so these now get automatically extracted, making it no longer needed to keep them in a manual.pot file. The only reason for me to have a manual.pot file that gets merged in, is to list message ids that cannot be automatically extracted. This warning helps me to clean up such a manual file.

Apparently you have a different use case, and adding the references like you do in the next lines makes sense then.  But I want to keep the warning. :-)