Any theme with that many options will have some type of difficulties and personally I completely understand.

We definitely need a better education and more tutorials how to "convert" to Customizer.

As far as the ThemeForest and WordPress.org comparison, I don't even know why mention, they're two different "beasts".

There should be a basic understanding out there, one offers 100% free themes and most of the times themes are built the way how themer finds it fit, while ThemeForest are tailored to sell, which doesn't mean it's better or worse from the other.