That's my gripe with Atomic distros. I feel like they don't take the time to think things through and throw together. Instead, they throw together a new thing to address the shortcomings of the previous five things.
Love them or hate them, it feels like the only player sticking to their guns is Canonical with snap. It's the only package manager that really does it all: GUI, CLI, IDEs, server, daemons, even the kernel and GRUB. Honestly, when the permission prompting is stable, I might be tempted to give it another chance.