The gnome extensions installed by default are in the Bazzite image composition, so if one of the extensions does break it will break for everyone using that image. If the Bazzite team catches it in the testing image then you won't have broken gnome extensions. However, due to the number of different configurations combinations of Bazzite available, it's not guaranteed that the team will pick up the an issue before it ships to stable.
Last I checked, if an extension is no longer supported it disables itself as it has the major and minor Gnome versions that it is compatible with coded in it's metadata. Sadly with gnome a lot of extensions tend to break whenever there is a major Gnome release.