Differences between Datasets and Reports

Cut your issue into smaller, more manageable chunks.

A PBIX file contains both the dataset data sources and their relationships  (aka the data model) and the user interface definitions (aka the report).  Once you publish that to a workspace they will be shown separately (but you can still download the PBIX from the workspace through either, and the components will be reunited).

If you refresh the dataset, either via schedule or ad hoc that will only change the data. It will neither change the data model nor the report.

If you are on a premium workspace and you have created an app and give your users access to the dataset via the app then there is another complexity.  The workspace dataset and the app dataset (as well as the workspace report and the app report) can get out of sync if you publish the PBIX to the workspace but then do not update the app. 

So do give access through the app, but remember to update the app if you made meta data changes.