One thing that I think is missing, or at least I am having an issue if this is not working as expected, is that Modify Server Config would actually read what the server has in it.
I screwed up my settings and change them back to default. I had a backup of the configs and threw them into the saved directory and I assumed these settings would appear in the Modify Server Config but nope. Nothing. It's all defaults. I would have expected that to import the setting that are in the ini files. I could help you with that code if you need it.