I'm in a similar position to the author—running NixOS on a Framework 13 for about a year—and while I agree with some of their points I think I disagree with others.
> However, this means that your projects end up populated with Nix files, which is particularly annoying when you want to submit PRs to upstream projects
This is a legitimate gripe, but it does have a mitigation, which is to add those files to your global gitignore. The trade-off you make here is that you have to explicitly add the files to repos that actually do need them, but that's a one and done cost.
> I'm now responsible for configuring this entire system. I am also responsible for updating this system.
On the contrary, I have felt much less responsible for configuring and updating my whole system since switching to NixOS. Most of my system is just whatever the upstream channels are doing. My whole system config is maybe 300 lines long, and most of that is a list of the programs I want installed, which is something that I've always wished I could have on other distros but can't.
On other distros I have felt much more responsible for controlling my whole system because random crap would break all the time and I had to learn how it was configured. That has never happened to me on NixOS.
Also, containers are totally available on NixOS and I use them all the time. I've avoided flatpak so far not because it's not available but because I want to try to do things the NixOS way and I haven't felt the need to move away from fully declarative.
None of which is to say that NixOS is right for you or anyone in particular, but so far my experience has been that there is a very steep initial learning curve that you do get over. Maybe someday I'll give Fedora Bluefin a shot, but in the meantime I'm definitely not regretting leaving behind the traditional distro model.