Please continue regardless of tech limitations
Hey, I'd just like to pop in and say I'd love to have a Flatpak-only app store, even if it has the technical limitation of only supporting user apps.
GNOME Software has a similar limitation of not allowing the removal of 'core' apps, even though these can be easily removed with the terminal. Most other platforms also don't allow removing some apps. While it's not great to limit the control people have over their apps, it's not an abnormal limitation.
The ability to install or remove apps in system with Souk is not important to me at all. When I install my OS, I remove all pre-installed (system) apps and install my own (user) apps using a script. I think most people don't care about the system apps being there, and the people who do will be able to manage them in the terminal.
Furthermore, if development of Souk continues and ends up in the hands of users, distro maintainers like the ones behind Fedora Silverblue can be requested to set up essential, 'unremovable' apps as system, and have all the other apps install when a user logs in for the first time, allowing us to manage them with Souk. Without Souk, there is not much reason for them to make this change, making this a chicken-or-egg problem.
I hope I've provided some good arguments not to halt development purely because of the listed technical limits.