Male have a keyboard hook feature, which should been exit MagicEngine when pressing ESCAPE, so no mouse is required there.
I mean there was some dos based editors seen at zophar.net, but how it is to day not really sure. If there is a document about these headers, it should been pretty easy to create a batch based tool do edit all roms based on the filename (pretty much that you see with ID3 tools today).
I remember I have tried a SNES on my Dreamcast to with many yaers ago, but not in fullspeed, even its a nice machine and you dosent need a bootchip to use homebrew software.