Right. I agree with most or all that you have written. But you have written about citizens, resident aliens or certain companies. What I said is that I do not know that it applies to non-citizens and non-resident aliens, i.e. a visitor, which would be who would be entering the US on the visa waiver. I am not saying it doesn't, I am saying that I am not sure that it does (res aliens, citizens and companies, I am sure about)

Cubans living in the US are actually allowed to go to Cuba as an exception to the embargo. Most US based legacy airlines, including AA, have flights to Havana, which, from my understanding, are very lucrative. A lot of them shuttle Cuban nationals. IIRC, they can go every two years.

I can tell you from personal experience that it is a total pain in the ... to get permission to go. I went through about 80% of the process and hit a brick wall. This was 2002 when the tightening and cracking down was begun. Things always get tighter at election time.

As far as the CUN-SCL question, I cannot help but question whether the computer systems are smart enough to look for through flights that happen to connect through Cuba since there is probably only one or two. That being said, does anyone really want to risk a $5000 or $10000 ticket on a computer being wrong? The rule is that you can't go through Cuba and, as I said, the treasury department is not going to care much about your argument that it was a through flight and not a stop or connection. Personally, I would go back through the US or take a short hop to Mexico City.