It’s not a flaw. Ostree is a last resort, you should be using containerized software. Layering a package should only be done when strictly necessary and not as the regular way to manage packages. If you need an overtly customized system, you use Nix or universal blue to design your new system declaratively and create your custom image.
That is a flaw. Flatpak is great where it works but Flatpak doesn’t solve all problems, neither does any one solution except os level modification. It can be a last resort by it should be a last resort that works. The layering system could be put together such that you don’t get side effects of installing packages like that. It might be tough to fix but that doesn’t make it not a flaw.
Please remember that no one is taking anything away from you. If you don’t like it, you don’t have to use it. Traditional package managing isn’t going away any time soon. You are safe. Others can have their preferred tech, and you don’t have to like it. It’s ok to have different tastes.
