The reason it's not a problem with tons of vehicles is because the way the vehicle is used.
Using DI vehicles for short trips is a no Bueno. Restart after restart after restart will build carbon up on the valves of ANY DI engines valves. This is a know FACT of any manufacture that makes DI engines; not just Ford. Oil and fuel fumes will build up over time on a warm valve when they are open after the engine stops.
Much like the turbo problems that the first gen 6.7 Cummins customers were experiencing it makes all the difference in the world on how one drives the vehicle. Many owners didn't know about this problem because they used their truck for heavy work. That didn't mean the problem didn't exist. It just meant those that drove their first gen 6.7 Cummins hard didn't have the problem.
You said: "I never heard of that with the 3.5L Ecoboost." When I give you a link that tells you about the problem you start talking about EGR's which have next to nothing to do with the problem. How do I know this? Because as you have pointed out, the 3.5 doesn't have EGR but still has the problem.
As far as being a "major" issue. I guess Ford disagrees with you because they don't pop out TSB's Willie Nillie.