Now, using snap store, flathub and all that is just unhygienic.
What is this based on? What do you mean by “unhygienic” anyway?
Flatpaks are more secure than system packages. They’re not installed with installation scripts that run as root (and can therefore do anything to your system if malicious code is slipped in.
Flatpaks also have sandboxing. It’s not a perfect implementation mind you, but it’s better than zero sandboxing.
Snaps is a bit more complicated, but sandboxing works if you have a fistro that uses AppArmour, so basically Ubuntu and some derivatives. Although who else would use snaps anyway lol. Flatpak won that fight.
I’m certain most of the failures will be in the new shiny stuff
I don’t know why you’d be certain of that. New stuff is generally designed from the ground up to be more secure.
Look at Flatpaks Vs repo packages.
Look at xdg-portals Vs 500 different implementations to do the same thing.
Look at the absolutely cataclysmic security catastrophe that is X11 compared to Wayland.