Hi Jeremy,
That's been my experience so far. Unless I'm missing something, definition queries are not yet support with the creation of the runtime content. Currently I keep track of the definition queries in a configuration file and apply them during the loading of the map in the mobile application.
FeatureLayer fLayer = layer as FeatureLayer;
fLayer.DefinitionExpression = "SUBTYPECD = 2";
Seems like some extremely core functionality that they are missing here....
I'm using the 10.2.6 runtime and I generate the .geodatabase file in ArcMap 10.3.1.
Kind Regards,
Kris Foster