perhaps a better idea would be to somehow (optionally) include the required inputs to start the software in software-lists, and adding an option to MAME/MESS to execute it?!

Yes, that might be better and QMC2 can then send this info to MESS if needed (or turn the option on in MESS if needed)
I suppose it would be like the copy paste function with a few delays for the system to start up.

Do you think the team would accept this?