What they are warning you about is that if you use a URL and the query you give it uses the Related list querying you will not be able to open the breadcrumb to edit it until you remove the related list part of the query.  So basically its a user interface issue but the backend will use it properly regardless.

We do not have List v3 enabled and it works fine in the Reporting App which has the functionality built in whether or not its enabled which is why I went there to build the first query to get a copy for the correct formatting I needed.