Hello Jeff,
Thank you for the kind comment.
There is currently no way to run medInria from the command line to output composite images directly, the only current solution is indeed screenshots.
We have plans to add python scripting to medInria eventually, but for the moment we're still at the stage where we are modifying the core of medInria to pave the way for this, so it's still many months away.
In the meantime, you might have some success with a tool like Sikuli to script medInria :
www.sikuli.org/ .
I hope that helped, thank you for the feedback !