I'm thinking maybe the 10.5 release of ArcGIS Server was mistakenly coded to act like an ArcGIS Online subscription where I noticed in a recent ESRI MOOC two users are not allowed to name something the same (Organization-Wide).
Reading about ArcGIS Data Store 10.5, it seems like everything will get tossed into a single schema in the back-end.
Reading about Pro 1.4, it is currently not able to publish directly to an ArcGIS Server into its separate ArcGIS Server folders - It publishes directly to Portal for ArcGIS which then creates all map services in the root folder of ArcGIS Server. (Federated that is)
That would match the behavior of not allowing duplicate feature class names.
If this is correct and intended, it is a huge restriction to put on enterprise GIS/geodatabases.
A show stopper of sorts for ArcGIS Enterprise 10.5 at this time until workarounds and/or new supported ways of doing things are figured out.
If this is not a BUG with an immediate fix, it will force customers like us to completely change proven production workflows with ArcGIS Enterprise.
Hoping it is just a mistake somewhere on my part.
I'm working a case with ESRI support now.