MicroStation CONNECT Installation Question

When you install CONNECT using the Custom Configuration and redirect the ORGANIZATION location, the MSDIR.CFG still points the ORGANIZATION installation location to _USTN_INSTALLED_CONFIGURATION=C:/ProgramData/Bentley/CONNECT Edition//Configuration/.  This contradicts what I pointed to during the installation, so my customized WorkSpaceInstalledSetup.cfg is never read.  Why doesn't this point to my redirected location? Are we really supposed to edit this after the fact?  I understand that you guys are putting a default installation in PROGRAMDATA location, that is a great idea, but I don't want to read anything from that location, I want to read from my custom CONFIGURATION location.