Yes each entry in the ssh config file has its own IdentityFile entry with the full path to the key file. Maybe it’s because they are indented an additional level more than the HostName and User fields it’s not recognizing them?
I think to apply you would need to remove the config entry in xpipe and search for it again.
About the reimport, you can right-click the SSH config root, remove it, click on the magnifying glass button on the local machine to automatically add it again with the latest info. But I can fully understand that you don't want to do that, dealing with unintuitive interfaces isn't fun.