Fedora with Flatpaks is open and up front about whether you're getting a Flatpak or a system installed package, and lets you choose if both are available. And installing through dnf/yum isn't going to do anything at all with Flatpak.

And what about Debian with debs? That's literally what apt was designed to work with. If it gave you Flatpaks, or the flatpak command installed debs, that would be more like what Ubuntu is doing.

The fact that Canonical shoehorned snaps into apt is the problem. I've heard bad things about snap, but I wouldn't know because I've never used it, and I never will because of this.

When I tell my computer to do one thing and it does something completely different without my consent, that is a problem, and is why I left Windows. I don't need that in Linux too, and Canonical has proven they can't be trusted not to do that.