So I just tried this. I took the stock boot.img for November and patched it in Magisk. It said "backing up stock boot image", but there is no new file in /data. I see old boot.img backups in that folder that Magisk made, but not the one it supposedly just backed up.I think the issue is the order you are doing your steps. If you let Magisk modify the stock image prior to flashing the update, the update will overwrite the Magisk backup. You need to flash the update before you use Magisk to patch the stock boot.img.
You can confirm this by checking the location of the Magisk backup. It is located at /root/data in a file with the name "stock_boot_XXXXXXXXXXXX.img.gz". Using your current steps, if you check for the file after patching the boot.img, I think you will find it. However, once you flash the update, I'm sure that file will be erased. This is why Magisk is failing when you try to unistall it for an OTA.
To fix the problem, just "install" Magisk again. Open the Magisk manager app and press the Install button next to Magisk (even though it says it is up to date). Choose the "Select and patch a File" method and select the correct stock boot.img file that you previously extracted and moved to the phone. This will force Magisk to recreate the patched file and create a backup. Once that is complete, you can stop. You shouldn't need to actually reflash the modified boot image again because Magisk is already installed.
If I attempt to use Uninstall > Restore images it says no stock boot image exists.
I also just restored Magisk Manager to the default apk, and that didn't work either.
I'm using Magisk 20.1.
EDIT: Thanks to this post I was able to find the backed up stock boot image. It's in /data/user_de/0/<package name>/install/. I copied this backup to /data/ and I am now able to uninstall Magisk and restore the stock boot image. I should be able to take the next OTA now (hopefully).
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