I am a Mechanical Engineer who works on the design of the Auto EDS, which is the equipment that everyone's "checked" luggage is scanned with (ever since 2002). I can't disclose too much without the men is suits showing up at my house and taking me away
, but I can say (this is public knowledge), that they are CAT Scan machines programmed with 1000's of algorithms to detect all kinds of shapes and specific weights.
It doesn't matter where you hide your stove or fuel bottle in your luggage, these machines will still see it. If it detects something, it alarms the bag and it is diverted for a hand search down in the bowels of the airport. If the TSA screener finds your stove, or especially your fuel bottle, it's at his/her's discretion on whether it is a threat or not. If they find it a threat, you will find a note from the TSA in your luggage stating that they have confiscated your item. If the screener deems it a no threat, you will never know they even searched your bag, unless you had your bagged locked and now find the lock removed with some possible damage.
Bottom line is you risk confiscation every time you fly with these items in your checked luggage, though if they are cleaned well your likely not to have a problem. The best advise I can give is to clean your stoves the best you can, and try not to fly with fuel canisters even if they are clean. The shape alone can trigger an alarm, which could cause for a hand search AND the possible confiscation of your clean stove (which might have passed un-noticed). Personally, I would rather throw out (2) $9 used fuel bottles, than have my $120 stove confiscated after an awesome trip...