kind of reminds me when i tested the 64GB emmc deck with bazzite ages ago. it would not shut down properly, but it was plagued with so many issues besides shutting down improperly
btw i dont have a fix. i would make a #bazzite-help thread if it really bothers you or make an issue in our tracker on github. this isn't too bad of a workaround though. next time you want to update, go into desktop mode > open the System Updates application and shut down from desktop
when it comes to suyu i would wait until get get accustomed to the code more, right know i would imagine they are trying to figure out the code and would consider it unstable. can instead use archived versions of the old program