Manage Configuration vs. ConfigurationSetup.cfg

Our firm utilizes MicroStation CE Update 17 as well as OpenRoads Designer 2021 Release 2, both of these share the same WorkSpace. I want the installation of these products to be as simple as possible for our IT folks, so I have been utilizing the options during setup to point to the Custom Configuration. Once the program is pointing to the Custom Configuration, I want all the other custom items to be handled within the workspace. In other words, I don't want to have to make further adjustments to users local machine to point to different aspects of the workspace. 

Everything seems to be working for ORD, but it seems like MicroStation is no longer honoring the ConfigurationSetup.cfg settings pointing the _USTN_CUSTOM_CONFIGURATION variable to the folder that contains the WorkSpace.cfg files. I was then reading about the Manage Configuration included with MicroStation Update 17 and am wondering if it is now conflicting with the .CFG file. This may be a pretty broad question and I'm more than willing to provide additional information to get things on track. 

Does MicroStation always defer to the .XML that is edited by the Manage Configuration tool? Or only after the tool is used once? I don't recall this being an issue, but it seems a couple of users are now not seeing the Workspace unless that tool is used to point back to the custom configuration folder manually. This is not something I would like users to do on their own for obvious reasons.

Any ideas?

Thanks,
Ken