Your idea of putting a flat on the truss rod and anchoring it with a set screw should work fine w/loctite etc.
You can try the "flat with set screw" idea but it didn't work for me. I ended up peening the anchor end as stated in a previous post. Others weld it. There is ALOT of stress on that anchor/truss rod connection.

As for putting a flat on the end and weakening the rod....yes it will weaken it. But in theory as long as I have a larger cross sectional area than the minor dia of the threads it will still be stronger than the threads. So if something would happen to break it would be the threaded area again (in theory
)