Applescript - Run Multiple Instances of an App in Mac OSX
You would need to compile your own transmission-daemon to be able to run multiple instances. Once you have done this you can specify different ports on each instance and start them up. 

Information on compiling your own transmission-daemon on osx can be found here: 

https://forum.transmissionbt.com/viewtopic.php?t=7532&amp;p=52071

How to run multiple instances of transmission-daemon: 

https://forum.transmissionbt.com/viewtopic.php?f=8&amp;t=9139