- Does this mean the Add On Manager is actively applying the tweaks to P3D?
No, until you press the "Save to Prepar3D" button.
Can these tweaks be overriden if I make changes to p3d.cfg?
They ARE what you already have in your P3D.CFG, the Addon Manager is nothing more than an interface to edit that file. There's nothing to override, the sim only sees the .CFG file so, if you edit a value in the .CFG file manually, you'll find it just the same in the Addon Manager the next time you start the sim.
If I dont want to run any tweaks on my setup, how can I disable the tweaks in Add On Manager?
As I've said, if you see those tweaks, it means that this is what P3D is already using, because they are taking from your file. Even if you don't have any tweak, it doesn't mean there's no tweak active, it simply means the sim is using a default value for it, so even if you would write them back using the Addon Manager "Save" button, even if you now *see* the tweak, the end result would have been the same as if there wasn't any tweak to begin with, because the sim were using the default value (which is the same the Addon Manager starts with) in any case.
So, the only case when you really are affecting things (for good or bad, it depends on your system and settings), is when you MOVE an Addon Manager slider AND press the "Save" button to write the .CFG.