Anyone who has heard my SQL Saturday presentations knows I don't much care for XML and this is one of the reasons. A trick to using XML configuration with varying locations is to use an environment variable (indirect configuration) to direct SSIS where it can look for that resource. The big, big downside to this approach is you'd generally need to create an environment variable for each set of configuration files or have a massive, honking .dtsconfig file which becomes painful for versioning.
The option I prefer if XML configuration is a must is that the "variableness" is removed. Developers and admins get together and everyone agrees "there will be a folder everywhere SSIS is done to hold configuration files and that location is X" and then it's just a matter of solving for X. At a previous job, we used D:\ssisdata\configs
@HLGEM's approach of a table for configurations is hands down my favorite approach to SSIS configuration (until you get to 2012 and their project deployment model where configuration is an entirely different animal)