Given that the Bad Guys ™ were in the front of the airplane and therefore at the scene of the impact, I’m pretty sure that, even before the fire started, they were
- Crushed by the impact
- Sliced n’ diced by flying debris
- Hi, Opal!
Then, any fire hot enough to melt steel is going to incinerate the mortal remains. So, I’m pretty sure that the hijackers are dust and ashes.
Even so, I would rather carry out every body bit under a flag as a way of showing respect to the dead, and chance there might be a fragment of hijacker beneath it, than to start arguing about who “deserves” the honor. The odds are so much greater than any bit found that can be identified as human flesh is an innocent that, to my mind, it’s not worth worrying about.
Now, about the foreign nationals… if, hypothetically, I was killed in a foreign country and my body was carried out under the flag of another country I can’t see where I would be offended. It is, after all, a sign of respect. You do that for heros, usually, and certainly not for your enemies. If, hypothetically, I was in France or Germany at the time and died in an attack on their country… nope, while I’d prefer my own flag, can’t see how it would be anything other than an honor to lie under theirs.
I would imagine that, had we been able to know that a particular body was a foreign national we’d use their flag or whatever is considered appropriate by that country, but most of 'em were found in, um, pieces and that after several weeks of lying about and, um, well, I’m sure actual recognition is going to rely on medical recods.