Linux distros usually raises a reboot required flag. But thats usually to complete some kernel or system update. Windows just go ahead and reboot on update ruining the workflow.

When you get the message to reboot ignore it and do your work. Then shutdown after doing it. Turn on when you need it the next time. And its all well

There’s a configuration file you can edit to prevent that. The Flatpak configures this automatically for you.

“updates were installed, you should reboot”.

But I think you can ignore it, the updates just will not take effect until you reboot.