No EU compensation for sure. As mentioned, non-EU carrier departing non-EU airport. Who knows whether Bolivian law offers any recourse... I presume you are referring to Christmas or some other peak travel date because there are several daily flights from Madrid to Munich...

As far as being denied boarding despite making it to the gate, this has happened to me as well. No compensation, although I didn't fight it as hard as I should have. I suspect that somewhere you can find fine print that says that you need to be at the airport a certain time before departure, not just the gate. This is well-known for clearing security at Heathrow, but less known elsewhere. Considering that Iberia will have known that they weren't on the hook for your late arrival, they will have taken the decision to offload you and get somebody else on board.

One good way to see whether your case has any legs is to offer it to a claims company. If they can't be bothered, then you know you won't get far...