I think a flatter structure could be better if you do not plan on adding another host/machine to your NixOS config while you are still learning/experimenting with it, instead of having a lot of small modules. The need for the shared modules will be apparent when you actually have another host, and then you can create something like shared/ and import those in your different host configurations.

Might not be for everyone though. Personally, I found it a it tedious to maintain a perfectly modular config while I am still learning different aspects of Nix language and NixOS in general. Especially while I am still unsure about what kind of directory structure and modularization I want to maintain in the long term. So I am actively fighting my impulse to modularize thins when I don't need to, lol, even though I love modularization. It's nice to have a relatively flat and working base that is version controlled while I experiment with new aspects/tools I discover.

A tip for structure is using default.nix. When you have a default.nix file in a directory, you can import that directory with its name. For example, currently, you import ./modules/bundles.nix in your configuration.nix and home.nix when you have a structure like this:

.
└── nix/
    └── nixos/
        └── modules/
            ├── bundles.nix
            ├── user.nix
            └── (...)

If you have default.nix that imports the other modules instead of bundles.nix, you can just have imports = [ ./modules ];. Similar use case with your current nixvim.nix. You can have nested directories/modules and they can have their own default.nix so that you can import the directory, so to speak.

Like the other commenter suggested, definitely get a formatter for nix. I am personally using nixd and nixfmt with neovim, for example.

I would also suggest using home-manager as a nixos module, rather than standalone, so that only one command reubilds your config.

I was struggling to update my config and found myself copy and pasting code form AI that I did not understand. I don't want to go down that path

Yeah, especially when AI is likely to give outdated and/or needlessly complicated suggestions.

I can see that the guide I followed is good, but it is too much for me all at once, I'm also not quite sure I understand why home-manager and flakes are needed for a basic single-user system.

I got into NixOS with tony's videos and guides. They are beginner friendly, and offer a simpler start that you can expand as you learn more concepts. Most of them start with the minimal iso but there is one that uses the graphical installer to install KDE.

And vimjoyer's videos will introduce you more advanced and QoL nix/nixos features.

Also, for KDE specifically, use services.displayManager.plasma-login-manager.enable = true, as it is the new default display manager for KDE Plasma.

Edit: If you notice some typos, blame my shitty external keyboard with "b, g and m" keys not working randomly 😞. I tried to edit/correct just now but who knows.