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I would like the help of someone with more experience to understand the differences and how those 5 things are connected: libzypp, YaST, Zypper, PackageKit and Gnome Software Center.

Here is my take away from a day of research:

  • libzypp: the backend package management library that powers applications like YaST, zypper and the openSUSE implementation of PackageKit
  • YaST: it's a system configuration tool that happens to allow the management of dependencies through libzypp. It provides both a graphical interface (GTK) and an interface through the terminal (not sure what it's used here)
  • Zypp: the official command-line package manager of Open SUSE
  • PackageKit: that's where things get a little fuzzy for me. This seems to be a package manager abstraction - its supposed to abstract all the differences between apt, zypper, yum, etc
  • Gnome Software Center: it's a graphical interface (GTK) to install dependencies through package kit - so it's supposed to work with all distros, regardless of the underline package manager used

If I understood this correct:

  • Why don't I see the apps installed through YaST in the Gnome Software Center and vice-versa?
  • Why would I want to keep Gnome Software Center installed if the previous point (^) doesn't happen? To me this thing just seems cluttered
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I think your understanding is globally correct, even if I can find some differences in definitions :

  • Per Wikipedia, ZYpp and libzypp are the same thing i.e. a package manager.
  • Per Wikipedia again, ZYpp powers PackageKit implementation for openSUSE and SUSE Linux, YaST and Zypper.

Zypper provides a command line interface to use ZYpp.
YaST provides a graphical interface to use ZYpp.
PackageKit provides a unified way of using ZYpp and other package managers such as APT, pacman, YUM...

GNOME Software aims at being an application store, like Discover in KDE world. Its first idea is not to manage packages (like YaST or Synaptic) but applications.

GNOME Software uses PackageKit to interact with the distribution's native package manager. However, both are independent and can be used in other contexts.
For example, you could use GNOME Software to manage Snap and Flatpak applications, without PackageKit to interact with the native package manager.
Or if you use KDE, you will typically let Discover interact with PackageKit instead of GNOME Software.

So when you want to install an application, we could imagine the message cascading like this :
The user asks GNOME Software to install the application.
GNOME Software forward the request to PackageKit.
PackageKit forwards the request to ZYpp (because we are on openSUSE).
ZYpp actually install the application.

I hope that this clarifies the questions that you might still have...

So, getting back to your questions :

Why don't I see the apps installed through YaST in the Gnome Software Center and vice-versa?

You should see them if PackageKit is correctly installed and GNOME Software is set up to use PackageKit.

Why would I want to keep Gnome Software Center installed if the previous point (^) doesn't happen? To me this thing just seems cluttered

You might still want to keep GNOME Software to manage Snap, Flatpak, GNOME shell extensions...

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Definitions

Note that this isn't a support forum.

Gnome Software Center: it's a graphical interface (GTK) to install dependencies through package kit - so it's supposed to work with all distros, regardless of the underline package manager used

That is broadly correct. However, its name is now merely "GNOME Software", and not all package managers interact with it via PackageKit, due to PackageKit's deprecation by its developers.

Zypp: the official command-line package manager of OpenSUSE.

That would be zypper, on the CLI.

AppStream

AppStream manifests provide information like screenshots and logos.

Why don't I see the apps installed through YaST in the Gnome Software Center and vice-versa?

Whether you see certain packages installed via zypper or YaST in GNOME Software is dependent upon whether those packages contain AppStream manifests, because GNOME Software does not display packages without such manifests.

Consequently, some you shall see some in GNOME Software, but some you shall not. You should see all in YaST, however.

Why would I want to keep Gnome Software Center installed if the previous point (^) doesn't happen? To me this thing just seems cluttered.

Whereas YaST does not support rendering most of the aforementioned metadata, GNOME Software (and its Qt counterpart, KDE Discover) do.

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