Are you talking about paying with points, or charging your Amex on the portal? If the latter, you don't even *need* to use the portal with the Amex Platinum since it gives 5X points on airfare whether you use their portal (which is just Expedia, really) or direct through the airline. Given that, I'd book direct every time if paying cash and not points.

With other Amex cards, you will get some bonus for using the portal (particularly Gold, I think), and you have to ask yourself if the bonus MR points are worth it.

As soon as you get a third party involved, the potential for fingerpointing starts. The airline says it's the OTA's problem, the OTA says it's the airline's problem. And you are stuck in the middle, less concerned about whose problem it is and just wanting it *fixed*.