I see the same behavior with ArcGIS 10.3.1 and SQL Server. It is arguable whether what you are experiencing is a bug, design limitation, or simply the design of query layers. As is discussed in the documentation:
What is a query layer? A query layer is a layer or stand-alone table that is defined by a SQL query. Query layers allow both spatial and nonspatial information stored in a DBMS to be easily integrated into GIS projects within ArcMap. ... Query layers allow ArcMap to integrate data from geodatabases as well as from DBMSs. .... |
The focus or primary purpose of query layers is accessing data from DBMSes, i.e., not geodatabases. If you are using ArcGIS Desktop to access data in a geodatabase, the assumption is that you will be using the normal way of adding data into the application and not query layers. The New Query Layer dialog box uses SDE connection files to get DBMS properties, not geodatabase properties, so the version the SDE connection file is pointed to is basically ignored.
I am not defending how this works, or doesn't work, I am just explaining that what you are seeing is expected given the current implementation of query layers.