John,
I am out of the office until Wednesday but to a couple of quick answers.
I didn't have to uncheck any of the autorun options. As long as I connected to the A15 first, ran the reset function and then connected to the M4 before loading on the M4 I was fine.
You could have the A15 GEL file automatically reset the M4 but getting the M4 one to run the reset function would be problematic. You could create a little DSS script to do it as that could run actions on any core (including running functions defined in the GEL files).
Regards,
John