For certain low level applications, flathab may not work but for most cases, flathub is fine.
The second scenario is for something not even in flathub but is available in the aur which is signal desktop beta. The other day I installed this by typing paru signal and scrolled up and found signal desktop beta right there and pressed the appropriate number to install. This is much more efficient to install. If I were on my friend’s linux mint computer I would have to find the github and follow instructions to manually add the package.
I am comfortable doing both methods but my point is that users generally want the lowest resistance to new technology. Linux is supposed to be efficient and easy to use not having to look up guides when the Windows way is downloading and running a simple .exe.