That is a good point. I made the assumption was that these circumstances when these comments would appear was when the Gemfile was generated within an engine. However, I think you are right that that is not a correct assumption.

The main point I am trying to convey is that the current comments are not a good guidance when used in an engine. There are circumstances in engines where declaring gems in the Gemfile is the right thing to do. In particular for gems that are only used in one non-production environment (e.g. test).