dtexec has a parameter for specifying the config file to use. Shouldn't that solve your problem?

From http://msdn.microsoft.com/en-us/library/ms162810.aspx

/Conf[igFile]filespec

(Optional). Specifies a configuration file to extract values from. Using this option, you can set a run-time configuration that differs from the configuration that was specified at design time for the package. You can store different configuration settings in an XML configuration file and then load the settings before package execution by using the /ConfigFile option.

You can use the /ConfigFile option to load additional configurations at run time that you did not specify at design time. However, you cannot use the /ConfigFile option to replace configured values that you also specified at design time. To understand how package configurations are applied, see Package Configurations and Behavior Changes to Integration Services Features in SQL Server 2008 R2.