I am thoroughly confused, and must do some more reading.
Here's what MSDN Understanding Integration Services Package Configurations
In SQL Server 2008 Integration Services, package configurations are applied twice, before and after applying the options of the DTExec command prompt utility. This should be seen as an improvement, since you can now use the /SET, /CONF or /CONN options of the DTExec utility to alter the original definition of the configurations.
That seems to state quite clearly that you can now (in 2008) do more with the command line than in 2005.
But this is contradicted elsewhere: dtexec Utility
says when describing the /configfile option
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.
but then goes on to say
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.
Those two statements come one right after the other: "You can change things"; "You can't change things, just add things that you didn't previously specify". One can only wonder whether the authors are doing their best to confuse!