After looking at the command line version I am guessing it will program the first teensy 3.1 it finds. I don't think it is a limitation of how it was programmed, more a limitation of how to address the teensy you want to program. I could see if being done if you could control the USB port activation via another means, but that would be dependent upon the platform.
I am not sure if you can say control a USB port via script or not. I know you can do some things via some Python extensions, but I don't know if a port can be shut off. It might be worthwhile to figure this out for an automated programming system, but just for convenience this is overkill.