For those not following on the Ubuntu Community site, the root cause is confined applications seeing different gsettings configuration defaults to unconfined applications. This is due to the confined app seeing a different set of gsettings schemas to the rest of the desktop.
For instance:
$ gsettings get org.gnome.desktop.interface gtk-theme
'Yaru'
$ snap run --shell gnome-calculator
...
$ $SNAP/bin/desktop-launch gsettings get org.gnome.desktop.interface gtk-theme
'Ambiance'
This isn’t a snap specific problem, also affecting other confinement systems like Flatpak. We can probably work something out that will mostly do the right thing on most Ubuntu releases, but there is no general solution without e.g. enabling a different gsettings backend that does the settings lookup outside of the sandbox.