I've been using Linux since forever. As time goes by, I try to simplify my computing experience with less software, not more. Especially, less hugely complex software.
For example I'm not using KDE Plasma nor GNOME, but instead I use i3 (window manager) + a few simple helper programs. Or SDDM that I replaced with startx. Disabling Plymouth. That kind of stuff.
Flatpak as you guessed, go against that philosophy, adding another layer of complexity and overhead. I would agree with complexity to a certain degree: yes, you have to use another binary to launch your applications. But then again, rpm is also adding complexity to your system. You could also just compile everything from source and you would not have to have rpm installed at all.
rpm just has a packaging complexity. Once a rpm package installed, the program runs just as if you compiled it from source. Flatpak adds a runtime complexity, with its filesystem layering, permission system, integration with the base system and more...
It also goes a bit against the concept of a coherent whole as we have now. What I am aiming at has nothing to do with misplaced minimalism for the sake of minimalism. For example, I do not care much that the distro pulls a ton of recommended packages (by default) that I never use. I fail to understand your point then. If you don't care about bloat by getting a ton of RPMs, what is the issue of getting your applications via flatpaks (which are according to you bloated as well)?
I don't care about disk bloat. That is, packages installed on disk that get never used. I care about runtime bloat, or "added complexity" as I prefer to call it, which I would file Flatpak in that category.
I'd also like to add that the whole story is imho very coherent: the base OS will be RPM based and most of the applications will be added on top via containers and flatpaks (at least that's the current-very-in-flux-state-of-the-art). It's just a different story than it was before.
I hope that Flatpak will be limited to a few huge desktop programs. And not something like kcalc or gedit...
To get back to Flatpak, I do not deny it may solve real problems. But I absolutely do not need it on my PC, for my usage. I don't need to run Firefox, Thunderbird or some other desktop program containerized. You don't, but from a security standpoint, you really do want to run your browser as isolated from the rest of your system as possible.
Firefox already has its own sandbox model already and has an AppArmor profile. How many layers of sandboxes does it need and where does it stop putting boxes into boxes to run software ?