I've taken my alcohol stove on airlines plenty of times. TSA people don't even know that it's a stove and it's never been taken away. However, they have taken away a nice MSR whisperlite from my dad's luggage which was unused and still in its factory packaging. They claimed that it could have had gas still in its pipes. WTF? I think what they mostly do is just a visual identification to check for stoves in your checked luggage. I wouldn't worry about a blackened pot bottom at all. They might be able to "sniff" for explosives like white gas and propane, but I doubt the same technology works for an alcohol stove, particularly if you're using it with isopropyl, which your blackened pots seem to hint at.
Anyway, my guess with the bushbuddy is that since it does not look like a traditional camping stove, you're probably safe.