There were two tests here for determining that the sniff was constitutional. One was the level of inconvenience that the suspect would have to endure (the fear that it'll let cops put suspects "through hell on a hunch").
The second was the amount of private information that could be gleaned from the process alone. X-rays, infrared scans, phone taps, etc, would all allow officers to learn more than whether or not someone has done something illegal. (This is why I came out against collecting the DNA of all arrestees in this thread. Someone in that thread pointed out that the inconvenience is minor, but I still found it abhorrent because the information gathered from a DNA sample goes far beyond whether or not someone is breaking the law. This ruling addresses both issues.) No proper reading of this ruling would allow the use of any of the other methods you listed without a warrant.
If you can search everything, then search everything.
You can't search everything. You can search smells... And not even all smells... since the court wouldn't have allowed the search if the dog was let into the man's car, you're just talking about smells that drift into the public... and you're not even allowed to do anything with those smells except determine whether there's an illegal substance present. If the dog sniff could let the officer know the guy's shopping list in addition to the location of the large stash of illegal contraband this guy was carrying, then the search, like the thermal imaging scans in Kyllo, would have been unconstitutional.
The only 'cause' mentioned was that the suspect appeared to be acting 'nervous' - whatever that means.
You haven't read the ruling... or at least not the footnotes. Caballes acted nervous, his car smelled of air freshener, and he said he was moving but only seemed to have a couple sports jackets in the car. Now... that wasn't probable cause. Nobody claims that was probable cause. If the officers thought those actions gave them probable cause they would have opened the trunk without first bringing out the drug dog.
But the court found that even without the "vague hunch" they got from Caballes' actions, the police were justified because the dog sniff did not invade Caballes' privacy.
Now, if you actually knew of scientific evidence that the drug dogs will react to Puperoni treats in addition to illegal substances, you might have a privacy case.
What if the dog is simply trained to sniff for "car"?