The Stack Exchange (SE) community is for Questions and Answers. Thanks @ScottWeldon for useful links. Let's look at the Questions and its relation. The Questions might be the same or similar. The example of the same question is in the my question above.
The main point is that different SE sites is the different communities, so each question might be more than one site, especially of it is the crossover question.
But Questions in different community could be targeted to different points of view. So, I think, good practice for the same Questions' answerers now is to give Question a comment with link to the same on different SE site. For similar question this might be point of interest to view another Question and Answers (Q&A). So, the good practice is to make a link between similar or the same Questions.
The Answers on emacs.SE or Stack Overflow have different direction, so it cannot be just joined and Question be set as one crossover question. The crossover Question might be one (in my opinion), but the Answers must be divided into the separate communities with links, of couse. Or the Answers might be marked with community label etc.
Closing by off-topic reason have enough clarification in Q&A and Help sections of the SE community. This links between the sites could be the first stage of the mentioned crossover questions.
And for askers: before asking a Question, good practice is to make a search through SE Q&A and gave in your Question information about why the similar or looking the same Questions is different from you. If there is no difference why you are asking for?