The documentation doesn't state which of them should be used by default for new apps. Is there any reason not to still use PortableApps.com Installer?
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By launcher, do you mean the PortableApps.com Menu, or the thing commonly referred to as a launcher?
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portableapps.com_installer vs. portableapps.com_launcher
You use both.
First the Launcher (after creating your file structure and .ini files necessary). This creates the AppNamePortable.exe which is what the menu runs.
Then the Installer, which packages the portable app in paf.exe format for installation by the menu.
It's not the same thing.
Launcher is used to "create" a portable application.
Installer is used to compress the portable application to distribute it here.