installing Chromium
This wouldn’t sit well with most privacy conscious folk out there. Though, I can understand it from a security point of view. Especially, when one notices that Chromium isn’t installed from Fedora’s repos, but instead the RPM is built to offer a more up-to-date version that should provide improved security compared to the stable version.
removing Flatpak
Probs for the sake of disabling unprivileged user namespaces; as you might have correctly alluded to.
even software stores
I imagine for the sake of minimizing attack surface.
So how am I gonna install software now, layering?
The Nix package manager is installable on Fedora’s atomic distros, so perhaps that route is worth exploring.
to my knowledge flatpaks are more secure than RPMs
To my knowledge, Flatpak’s sandbox indeed isn’t achievable by default with RPMs; unless one knows how to properly utilize SELinux to that effect.
Pop!_OS is definitely worth considering as it’s one of the few distros that goes as far as providing a recovery partition and offers one of the best experiences for those with Nvidia GPUs. Furthermore, Pop!_OS’ maintainers (read: System76) are actually financially incentivized to make their distro very polished and newbie-friendly as their distro is used on the hardware they sell.
On the flip side, Pop!_OS is currently in a major overhaul to replace GNOME with COSMIC; their own homebuilt Desktop Environment. As the Desktop Environment is arguably the most important contributor to how one experiences their Linux system, the eventual change might disrupt your workflow and you might even be too accustomed to GNOME to consider COSMIC at that point. The ongoing work on COSMIC has even meant that Pop!_OS has missed three major releases and are still clinging on their release from April 2022; thankfully it’s based on Ubuntu’s LTS (read: Long Term Support) release, so they aren’t particularly in rush to get a new release out and can rely on Ubuntu for security updates.
Regardless, COSMIC’s unsure future does leave a lot to be desired and does pose the question if perhaps other options should be considered more seriously instead.
Therefore, my personal recommendation would be either one of the following:
A shortlist of distros worth considering for a beginner (from easiest to hardest): Linux Mint, Ubuntu, Debian/Fedora/openSUSE and Arch.