Hi Scott, great articles for the SSIS configuration.
I was testing your code on my machine and found out that:
When I try to add a new variable in the package and map it to configuration using BIDS configuration wizard, it will update all the config value from the variables default - This is actually the default behavior. The problem is there will be administrators using BIDS and try to fix something on the production server (don't ask me why - ok the answer is because it's convenient) they will inadvertently reset all the production value to development value settings from the package... This is true happen on file base configuration too, it's just that I got myself into this problem before and luckily I have the config file backup. In your new SSIS config settings we'll need to get it back from history table so writing a restore script might be a good idea.
My 2 cents is "Do not try to add configuration changes on production server using BIDS."