I don't think using environment variables for most configs is a good idea. Perhaps one or two to point at the config server and database. My major opposition come from the issues changing the values and that they are not particularly visible.

I also think it is a bad practice to modify, in any way, a package that has been released from Dev. When you do, you can longer trust your testing, as the package has changed.

Also, I swear that there is a property at the package level to supress those warnings. At least in 2008 there is..

CEWII