SUMMARY
The issue: the way kwin tracks window icons is different from how icon-only taskbar does it. When specifying StartupWMClass in desktop file of an app, icon-only taskbar considers it when picking an icon for the application, but kwin does not, which makes the way kwin tracks window icons inferior to how icon-only taskbar does it.

The way GNOME tracks window icons also seem to respect StartupWMClass [1][2].

For me, the issue occurs with the following software:
- Ente Auth (https://aur.archlinux.org/packages/ente-auth-bin)
- Signal Desktop (https://archlinux.org/packages/extra/x86_64/signal-desktop/)
- YouTube Music (https://aur.archlinux.org/packages/youtube-music-bin)

For all of them, the desktop file name doesn't match the WM class name, but the desktop file specifies it with StartupWMClass, which makes the icon-only taskbar use the proper icon, but not kwin.

STEPS TO REPRODUCE
1. Install and launch any of the software listed above
2. Look at their window icon, alt-tab menu icon and the icon in icon-only taskbar

OBSERVED RESULT
The icon in alt-tab menu and on the window decoration is the default Wayland icon, but the icon-only taskbar it is what it should be.

EXPECTED RESULT
The icon kwin uses for an application should match what icon-only taskbar uses

SOFTWARE/OS VERSIONS
Operating System: Arch Linux 
KDE Plasma Version: 6.4.5
KDE Frameworks Version: 6.18.0
Qt Version: 6.9.2
Kernel Version: 6.16.7-zen1-1-zen (64-bit)
Graphics Platform: Wayland
Processors: 12 × AMD Ryzen 5 5600H with Radeon Graphics
Memory: 16 GiB of RAM (13.5 GiB usable)
Graphics Processor 1: AMD Radeon Graphics
Graphics Processor 2: NVIDIA GeForce RTX 3060 Laptop GPU

ADDITIONAL INFORMATION
[1] https://github.com/ytmd-devs/ytmd/issues/2806#issuecomment-2584973530 
[2] https://aur.archlinux.org/packages/youtube-music#comment-1003960
https://github.com/ytmd-devs/ytmd/issues/2806