I was hoping this issue would be resolved before Exchange 2013 RTM CU1 was released, but apparently not. This only affects upgrades from Exchange 2013 RTM to RTM CU1.
During the installation of Exchange 2013 RTM CU1, setup runs a prerequisite check on the Exchange 2013 RTM server. Among other things, setup checks to see that required Windows features and roles are installed. If they're not, setup cannot continue and you need to cancel the installation to install the necessary prerequisites. The prerequisite check stage is also the last point where you can cancel the installation for any other reason.
Unfortunately, setup stops the Microsoft Exchange Transport service during the prerequisite check and does not restart it if you cancel setup to install the prerequisites. This means that email flow is affected prior to installing CU1.
If you do cancel installation for any reason after setup runs the prerequisite check, make sure you manually restart the Microsoft Exchange Transport service.