I change my opinion depending on which app it is. I use KDE, so any KDE app will be installed natively for sure for perfect integration. Stuff like grub costumizer etc all native. Steam, Lutris, GIMP, Discord, chrome, firefox, telegram? Flatpak, all of those. They don’t need perfect integration and I prefer the stability, easy upgrades and ease of uninstall of flatpak. Native is used when OS integration is a must. Flatpak for everything else. Especially since sometimes the distro’s package is months/years old… prefering distro packages for everything should be a thing of the past.