You’re thinking of just one extension, one instance. Now repeat this for EVERY single Gnome release, for pretty much all extensions (not just this one), and you can understand my frustration. Which is why I’ve left the Gnome ecosystem.
Also, it’s not like v45 came out of the blue, the beta releases were available for quite a while prior to final release, and even before the final, the Gnome developers did warn that about the upcoming extension changes. So it’s not like the Material Shell devs were unaware.
Edit: Also, the PR may have been merged but the updated version hasn’t been released yet. Both the versions on Github and the Gnome extensions site are still the old release.