I just went through a week of back-and-forth with ESRI Tech Support about this issue. I have found two parameters in the Defaults Keyword in the dbtune table:
Parameter: A_MS_SPINDEX; Value: "GRIDS = (MEDIUM, MEDIUM, MEDIUM, MEDIUM), CELLS_PER_OBJECT = 16"
Parameter: B_MS_SPINDEX; Value: "GRIDS = (MEDIUM, MEDIUM, MEDIUM, MEDIUM), CELLS_PER_OBJECT = 16"
One modifies the "ADDS" table default spatial index and the other modifies the "DELETES" table spatial index. I tried removing the value in each of these since the default for SQL Server 2012 is the GEOMETRY_AUTO_GRID. This didn't work. The Analyst at ESRI contacted a developer. The developer said "he wouldn't recommend using GEOMETRY_AUTO_GRID as the default." I asked him to confirm that he essentially meant that they hadn't programmed the dbtune table to allow for that. He agreed on that being the case.
I therefore posted an ArcGIS Idea requesting that the option to use GEOMETRY_AUTO_GRID for the spatial index and to allow it to be used by default. I am guessing it is only a matter of time before they realize what they are missing but just in case, go promote the idea.