Thank you.
One thing that is slated for development is the ability to assign arbitrary thread tag permissions to arbitrary ranks (via checkbox, rather than via drop down box as it is currently).
As for the separate sections, for those who really want to discriminate the sections out (
something I think is unnecessary), that's what "Classic Mode" is for.
Perhaps I can get a "cleaner" layout done in system.
As for your Application issue, this is with the applications, not so much with the forum. The application is creating a private thread for multiple recipients and just because you might be changing the rank of someone doesn't mean you're removing them from the private thread.
You'll want to head to Admin > Forum > Thread Tags, and make an "Applications" thread tag, setting the rank to the minimum rank you want to see the apps.
Then head to Admin > Applications and Recruitment, and click [Settings]. There you'll set the Application thread tag.
The newly created App thread tag will supercede private thread security, and demoting accounts will fix the problem.
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It's all in the reflexes.