With the current AutoCAD publisher (using native AutoCAD) it very hard to set the right options when you have to deal with specific settings for different locations/departments. The best way to deal with this is to create a separate AutoCAD profile for each location/department and to insert an AutoCAD block with all needed pagesetups (one specific block per location/department).
The profile sets the paths to fontfiles, ctb files and other references.
The name of the pagesetup is corresponding with the papersize.
The pagesetup holds all the details such as scaling, size, orientation.
With this two parameters we have the means to control all AutoCAD configuration parameters without extensive configuration within the publisher.