Are you using the Wayland session, by any chance? If so, then it sounds likely that you’re running into GNOME/gtk#1343.
Under Wayland, GTK selects its theme based on a configuration value stored in gsettings/dconf. If you haven’t ever changed a configuration value, then it won’t be present in your user dconf database and the default value will be taken from the gsettings schema. The problem occurs because snap confined apps see a different set of gsettings schemas, so some configuration values may look different.
So while on Cosmic the default value for gtk-theme might be Yaru, a confined application using libraries/data from Xenial might instead see Ambiance.
When you used the tweak tool to switch back and forward between themes, you’d likely no longer be relying on the schema default value for your theme. In turn you’d now see Yaru for those confined applications.
None of this applies if you are using the default X11 session though (or have X11 apps running throught Xwayland on the Wayland session). In that case, the theme name is communicated via the XSETTINGS protocol and should be consistent for confined and unconfined applications.
We don’t yet have a good solution for the bug I referenced. As a workaround, it might make sense to update the gnome-platform snap to set Yaru as the default theme in its schemas: this would make no difference to X11 sessions, and people using Wayland are more likely to be on the latest release rather than aiming for LTS stability.