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.
I don’t know what dependencies he has but my 3 year old system that is constantly being updated is full of flatpaks and all of the dependencies combined are only around 3GB. People see 1GB of dependencies and lose their mind.