You can load a blender instance from command line and pass it arguments, and execute a script inside blender to change images / audio files, and then render.
Your scenario describes it adequately:
- make a template blend file with placeholder audio file (a click track, whatever..)
- add placeholder images (test screens for example, with numbers to allow you to debug
- write the script that takes arguments (location of images, location of mp3)
- execute from command line
I'm sure if you provide such a representative template .blend file one of us would probably give you a hand writing the script to change out the audio and image files.
Alternatively you can script the entire animation, while starting blender from console with an empty .blend file (but with the script preloaded to accept a directory of images / audio ), this is also easy enough if you know Python.
See this answer for an introduction to commandline blender (no gui needed)