Rules created with the Facade Wizard are meant to work on 2D faces ( single polygons ), not extruded volumes. I see that your window objects are full (thin ) 3d volumes. This causes some issues of course.
What's inside or outside is defined by the 'normal' of the polygon. You can turn the normal to the other side by using the 'reverseNormals' operation.
But since ArcGIS does not really store topological information, bringing all that information over from ArcGIS can be a bit tricky.
Instead of bringing over a floor plan, I'd recommend to bring over 3d MultiPatches ( 1 polygon thick ), which represent 1 object, e.g. a wall, a window, ..
Then, assign a rule which constructs the geometry based on that 1 polygon and the rule.
Note that you can set the following 2 GIS attributes to automatically assign rule file and start rule.
ruleFile (string, e.g. "rules/wall.cga")
startRule (string, e.g. "Wall" )
That way, after the GDB import, you don't have to assign the rules any more.
You could even create an attribute for the normal reversing process.
doReverse ( boolean, true / false)
then in the CGA code, use that GIS attribute.
In short : You're much better off to import vertical flat shapes instead of the floor plan.
Let me know if this all makes sense.