I've added the AdwaitaLegacy (https://packages.msys2.org/packages/mingw-w64-x86_64-adwaita-icon-theme-lega...) icon theme which is the dependency of the Adwaita theme now.
This actually fixes the "different toolbar icon size" problem but I still think the smaller icons look better so it's worth considering to keep that patch too.
For more read about the "legacy" and "symbolic" icon problem, I recommend these long threads as a bedtime story:
https://gitlab.gnome.org/GNOME/adwaita-icon-theme/-/issues/288 https://gitlab.freedesktop.org/xdg/xdg-specs/-/issues/132