He's kind of discreet. / He's a bit secretive >> If you intend to imply that someone has a negative quality, you would mention that specifically. Saying "He's kind of discreet" doesn't necessarily imply he's a bit secretive. They're not polar opposites. "A bit secretive" isn't a character quality; it's a behavior. So normally you would say, "He's acting a bit secretive." Discretion, on the other hand, could be a character quality, but when you say "kind of" it's hard to know what you mean without more context. A better way to say this is, "He's usually discreet."
I'm getting annoyed by your attitude. / I'm getting uncomfortable by your attitude. >> Again, these don't necessarily express the same idea. The second sentence should read, by the way, "I'm uncomfortable with your attitude," and it doesn't have to imply that you're annoyed. A closer parallel to the first sentence would be, "I'm bothered by your attitude." But again, this doesn't necessarily imply that you're annoyed either. It could mean (for example) that you're disgusted or disappointed.
So, no, you can't use these sentences interchangeably; they aren't necessarily parallel to one another.