I noticed this bug in 1.1.1 and its still in 1.1.2 the skirt will go into the object. i think this is fixed if you make the skirt off set from object boundary instead of the footprint . i have attached screen shot.
We're going to try adjusting this for the next update, but yes, in the current release you need to specify a positive skirt offset that is greater than the width of the filament to make sure the skirt is offset from the model.
If you are using support material, the raft and skirt outlines will be based on the complete 2D "flattened" outline of the part, which is what you're looking for. So as a work-around, you could try enabling the "Generate support material" option and then just set the max overhang angle to 89 degrees. That way it won't actually create any support material, but the raft and skirt outlines will be able to extend all the way up without hitting the part. You could also just use a much larger skirt offset to ensure it doesn't run into the model overhangs.
I have been setting larger skirt offset as a work around it just gets annoying that i need to triple check the gcode for the skirt colliding with the part.