Clickbaity title on the original article, but I think this is the most important point to consider from it:
After getting to 1% in approximately 2011, it took about a decade to double that to 2%. The jump from 2% to 3% took just over two years, and 3% to 4% took less than a year.
Get the picture? The Linux desktop is growing, and it’s growing fast.
I’m not sure about the legal intricacies of it, but there is commercial software being distributed through flatpak on Flathub for a while now. The first example that comes to mind is Bitwig, a well-known, paid, commercial Digital Audio Workstation: https://flathub.org/apps/com.bitwig.BitwigStudio
Also, Flathub is working on offering paid apps: https://news.itsfoss.com/flathub-paid-apps/