All of my apps use configuration files, and not the registry, to save their settings.
The only difference between the portable and installer versions is a file called ConfigDir in the program directory which tells the app WHERE to store its configuration files.
For a portable install, it says to save them in the program directory; for the installer it uses a default directory, which will be under the users Documents\DonationCoder directory path.
In both cases, you can simply copy the settings file between machines to copy your settings.
In addition to a main settings file, FARR keeps some info in a couple of other files. There is a launchhistory.ini and a searchhistory.ini file, and custom aliases are in their own files.
All can be copied between machines.
The installer and portable executables are identical, the only difference is the ConfigDir file and which tells the app what directory to store its configuration settings in.