We recently had a health check with an Esri representative, to look at our Portal system. After looking at our ArcSDE enterprise geodatabase she said it was organized very well with everything put into its appropriate feature dataset. However, she then proceeded to tell me that she does not place feature classes inside feature datasets in cases such as ours, where we use feature layers in a federated server but DON'T use the data store. She stated that either method works, but she prefers not to put them in feature datasets in cases like ours because how the published features access the database.
We are moving from a test environment to a production environment, and I will be replicating our data over. Is it best practices not to put data into feature datasets and have them at the root level, will this cause issues with version edits, will it provide a benefit or ruin or data organization scheme?
-Portal - Federated Not Using the Data Store -Version 10.6.1 -Feature Layers are published and reference the enterprise geodatabase and are NOT hosted