The really hard problem to solve is making an UI where the simple thing is easy and the complex thing is still possible.
But that requires 1) strong leadership 2) people with the correct skill set for UX design.
Making a clean UI means cutting things out. And that's not easy in many large OSS projects because every menu item and every button is someone's pet feature. The leaders in the projects are often the most senior _developers_, not UX experts. It's (I'm assuming) a lot less common to have good telemetry and user labs in OSS than it is for commercial software. So you also might not know exactly what features people use and how they use them, making it even harder to remove features.
I think the author is absolutely right. If Handbrake is intimidating, or hard to use without reading a manual in order to do just the simple use case that 80% of users have, then they have failed in making a good UX. A good UX would make the simple thing easy without sacrificing power for the complex case. And the author is absolutely having the right idea when making a simpler wrapper for the powerful software.