[quote user="J-Worker"]How can I have MS_DGNLIBLIST in the PCF and the UCF without confusing MicroStation?[/quote]
Good News
The good news is that MicroStation is designed to work the way you want: it won't become confused.
Follow the advice you've been given. You can have a configuration variable point to multiple files or folders.
Bad News
There is no bad news!
MicroStation Help
Search MicroStation help for topic Configuration Variables. For information about the prefix and suffix operators search for Configuration Variable File Syntax.