They are as bad as i am making them out to be, at least for me :-P.
The core of the issue really - and Flatpak is just an attempt to work around it, not solve it, but just work around it - is that unlike the kernel the majority of foundational libraries do not provide stable ABIs.
As i wrote in another comment in this post, you technically can run software from the late 90s as long as that software is either statically linked or dynamically links only to the GNU C library and X11 (for GUI stuff), since the kernel and those two have stable ABIs since the 90s. However you do not get much functionality from those libraries even for a notepad-like application and anything beyond that tends to not provide stable ABIs.
And that is a cultural problem, not a technical one as there are several examples (including Windows as one of the most obvious) showing that you can have backwards compatibility and stable ABIs while also being able to extend the functionality of the underlying libraries (e.g. an app i wrote and compiled in WinVista got support for an emoji input box automatically in Windows 10 even though i never did anything for that beyond just using the functionality for text input that Windows provided since the late 80s).
Because of this the "(A)" solution you mentioned wouldn't even work since, say that everyone agreed to use -for example- GNOME. But that would only work until the Gtk developers decided to break Gtk's ABI yet again for their newest version, forcing everyone that decided to depend on them to waste time "upgrading" (the issues of which can be seen with XFCE or even better, Gimp that still depends on Gtk2 until at some point in the future when the Gtk3 is done - an move that a Gtk developer once described as upgrading from an abandoned version to a deprecated version).
I'm not singling out GNOME/Gtk though, the same issues apply with KDE/Qt since Qt also breaks their ABI every major version. If anything KDE/Qt are at a worse position by relying on C++ since despite how many promises GCC developers might make, with the C++ standard not providing a stable ABI promise, there is always the sword of ABI breakage looming over the head of any program that rely on dynamic libraries written in C++ (or any other language that doesn't have a stable ABI). Technically this could be solved by providing proxy dynamic libraries that use the old ABIs to forward calls to the new libraries but i am not aware of this being done in practice (i think Haiku does this to support BeOS binaries compiled with gcc2 but i'm not sure). I do not expect any C++ library to do that on Linux though.
So that is the root cause. It requires a cultural shift from often not even acknowledging the problem exists to actually considering ABI breakage something to avoided by all foundational libraries.
Flatpak is just a workaround that relies on the kernel at least not breaking its ABI, but even as a workaround it isn't that good for the reasons i mentioned. As i wrote in another reply, it could be improved - as a workaround, not a real solution - by only installing the libraries and software that doesn't already exist in the system and having better integration with it (with a large part of the latter being solved by doing the former). Fortunately so far most libraries do not break their ABIs every year, so at least chances are when i decide to download Notepadqq, it will use the Qt5 installation i already have in my OS instead of downloading its own copy.