So, to add physical servers into STM you'll need to install an agent on that server. I remember a customer having a script a long time ago, but I know I've since lost it. In other words, my answer is yes, it can be scripted.
Silent installer:
The agent installer does have a silent option. If you run the agent in command line with -? that will present you with a list of switches that you can run with the installer to set the destination ip address and set to run after install. If I remember correctly, the script the customer built had a list of IP addresses in it that were called by the script, then the file was copied to said server, and then the file was run with psexec. I haven't tried psexec with 2012, so, not sure how well that would work.
