The ES Loading graphic is unfortunately part of the binary. The only way to modify it is via the SVG file in the source code. If you want to change it, you must fork the source and recompile.

I suggest to you omxplayer and make a loading video that’s plays over the ES graphic.

If you figure out the Stella keys, let me know, also if the cmd line started Stella properly.

You can find all emulator command line starting code in ES_systems.cfg in /etc/emulationstation/