I tried signing my own keys. I replaced them in the bootloader, but when I do the final step to lock them down, the TPM chip flushes the new keys and reissues fresh keys again

It may just be that the firmware of your particular board is buggy to the point of being broken.

You could try updating it but sometimes it's futile and the firmware is just the biggest pile of crap.

Indeed there are many times I “need my hand held” in order to take my first steps into a subject. I need an intellectually-intuitive foundation that is stable and I can build upon.

Absolutely reasonable expectation. I wish we had that.

why a user owned directory in root is needed

I initially glossed over the fact that you said "user-owned" here. It still shouldn't affect anything because nothing uses /nix for anything security-critical at any point but it'd certainly be smelly.

User-owned /nix is only the case in single-user installs which I believe have been deprecated for a while and certainly aren't the way to go anymore.

These days the preferred and default method is a multi-user install where /nix is owned by root there and exclusively managed by the privileged nix-daemon.

What it means for NIX in reference to configuration files, dot files, and my mental model of mess that belongs in /home/$user. While unfounded, I immediately worry root will somehow get cluttered with junk too. It is probably wrong, but I think of $user being largely sandboxed in /home/$user/

Nix (the package manager) itself does have some limited local state (cache, current profile link) that is put into the appropriate XDG user dirs. It will never touch anything outside of those specific state dirs, the TMPDIR and /nix.

Nix is designed to be fully contained in /nix. This property enables you to even wipe their entire root on every boot under NixOS.

Apps installed via Nix behave as they always do w.r.t. cluttering directories. openssh will still create and manage its ~/.ssh directory for instance, just like on other distros. If you ran some daemon that you installed via Nix with sufficient privileges, it may try to create its state directory in /var or whatever; just like the same daemon from any other distro's package would.

That is all to say: Nix does not do anything special here. Its packages largely behave the same as they do on any other distro and that behaviour includes state directory cluttering behaviour at runtime.

I don’t know what the SELinux context is for NIX, but I only have a limited grasp of SELinux from hacking around on Android to add things like busybox, and I know it is permissive but enabled in Fedora.

No SELinux support whatsoever.
There is somewhat explicit non-support even as Nix' model of files and directories does not include xattrs; you cannot produce a Nix store path that has special xattrs for SELinux purposes.
Metadata like permissions, dates and owner information are all normalised in the Nix store. The only permitted metadata apart from the file name is whether regular files can be executed.

If your system uses SELinux, you must add an explicit exception for the Nix store. (Installers may do that automatically these days, I haven't kept up with that.)

question how anything placed directly in the root directory of another distro will impact future updates from the packagers of the distro.

Other distros simply do not touch /nix; it's not their domain.

FHS distros control FHS directories such as /usr or /bin depending on what individual packages contain but no sane package of an FHS distro will try to control /nix/store/hugehash-whatever/.

Isn’t this against the Unix framework to place something directly in root?

Nix does many things that go against original design principles of Unix and that's a good thing. It's not the 70s anymore and some aspects of Unix have not aged well.

https://economicsfromthetopdown.com/2024/02/17/nixing-technological-lock-in/

trouble with Nvidia with a mainline kernel and kobold.

Using Nix for applications that have userspace driver dependencies on non-NixOS requires a hack unfortunately: https://github.com/nix-community/nixGL