Yes, so long as the hard-coded path for the the config file is within the output directory, the program will find the right config file for that particular inst

Yes, so long as the hard-coded path for the the config file is within the output directory, the program will find the right config file for that particular installation. You still won't be able to put the config file in an arbitrary location, but at least you can have isolated instances of the program with isolated config files.