Being closed source is not relevant because running an external exe is an operating system process. I would also look into doing functionality like this just like real programming IDE's do. Save the code or changed textres/models in this case and then dump them back into the rom during the save process and have the build or run functionality call the emulator.
P.S. you can always use a decompiler to figure out the code of No$GBA. I'm sure there is a space in memory you can cram the pre-loaded rom into.