No worries Megiddo. That's not so much a contradiction as a correction. Being that it's so 'new', I just hadn't learned yet.
Since I'd not tested my theory, I didn't give 100% accurate information.
As for the whole slew of configuration files, wouldn't specifying commands in the config.txt overwrite previous ones already?
I could see instances where I'd want the slate clean so to speak, but most of the time, to keep things 'clean' in my mind, I'd rather just have the sub-specific game or map folders have less commands in them to keep track of what I'm doing/changing.
I guess it is a design decision that needs to be considered.
Possible way.. instead of having slate cleared, which MAY not be wanted by the user, make a clear command that can be run before other commands.
That idea mostly works with gimps, but, could be used for downloads/adverts too. As for the normal configs, I'd leave as is...just have the 'default' config items change only if specifed in the <sub_folder>/<map or gamemode> configs file.