It's an exclusive-or. You can trade with Cuba, and other companies that trade with Cuba, or you can trade with the US, and other companies that trade with the US.

Basically the United States will attempt to seriously penalize companies which trade with Cuba, though considering that large hotel chains like Melia can fully operate them and seemingly not face consequences, there must be some good workarounds or corporate firewalling...

Not exactly. Theres restrictions and penalties also for companies which trades with them and even for ships. They also cant use dollars in the trade.

I think the embargo extends to other WTO members.

May not right