The default behavior of GNOME Software is to automatically download and install Flatpaks, which are treated differently because of their self-contained nature. Native RPM packages, however, are downloaded in the background but require you to manually start the process of installation.
GNOME Software reboots the system into a minimal environment for offline updates, which is a stripped-down mode for safely updating software throughout the system. This offline update approach has a number of advantages:
There is a plugin for using an alternative method of updating: DNF5 Automatic. This sets up your system to check for and download updates at a specified time, then installs the updates in real-time on the live system after a randomized delay set in your configuration. Exceptions to real-time updates would include new kernels and the like, which always require a reboot.
This can be convenient, but you can also argue that there are benefits to manual oversight of the frequent package updates for certain system admins.