Gareth,
I've never tried this, but there is a way...
launch the ESTK from a command line, or system call, whatever the external app supports.
The following command line options for the ESTK *should* do the trick:
-run [filename]
This should launch the ESTK without a UI, and execute the file. The file will need to have a target directive (#target bridge).
Let me know if this works for you.
Bob
Adobe Workflow Scripting