In GeoServer 2.15.2 I can "publish" an entire layer from a GeoPackage. No issues there, works great.
However, If I attempt to "Configure a new SQL view..." using that same layer in the GeoPackage (or any layer from any GeoPackage), GeoServer fails to recognize "geom" as the geometry column. In the "Edit SQL view" screen, the "type" for "geom" is listed as "BigDecimal".
What I would like to do via the "SQL View" is to publish a layer from a GeoPackage and use a SQL query to scope the results (cannot do this if I just publish the entire GeoPackage layer).
Note: As I mentioned, GeoServer does indeed recognize "geom" when you "publish" the entire GeoPackage layer . . . it can successfully identify the geometry type and SRID. This fails when trying to "Configure a new SQL view...".
Update: GeoServer does not prevent me from creating/saving a SQL View layer using a GeoPackage as the "Store". However, it is useless because the geometry type and SRID are unknown (and the Bounding Boxes are populated with invalid data). However, if I manually edit the "featuretype.xml" file for the layer and populate it with the correct values, I can at least view it via "Layer Preview".