We did fix the publishing issue this morning with cooking scene layers with that hive so the original data could work now.
When you publish from a projected coordinate system you can select WGS84(4326) or the Projected coordinate system, in this case Web Merc(102100) on the publish dialog for the scene layer, depending on screen size/zoom you might have to scroll down a little on that dialog.
In the case where the data is in GCS 4326 you cannot select a local option at this time.