Good question.

There's one flaw though: If SSIS was installed at the same time as the named instance, there's nothing to do - the installation process does it all for you.

If it was installed after the named instance, but before the default 2008 installation, you will already have had to modify the config data to make it work at all before you get to the 2008 install.

If it's installed at the same time as or after the default 2008 installation, it will be set up to use the default instance's MSDB so the config file will have to be modified in these cases too.