This has been a big problem historically. Agreed.
But you cite the solution yourself. Flatpak is all you need for effective distribution of commercial apps. GPL has nothing to do with it. There are already commercial apps in FlatHub.
What is missing is “paid” commercial apps. We have no “take my money” App Store in Linux. I think FlatHub is working on it. Honestly, I am surprised a commercial company has not launched one yet. Well, other than Steam of course.