Wouldn't it seem logical to make just one installer per PortableApp and then have that installer download the setup file and extract it to the directory. Would eliminate the need to re-compile PortableApps when the base app is updated.
For example, let's say I had a Mozilla Firefox Installer. It would, upon launch, create the necessary directories and files for the general structure of the PortableApp, install the Launcher and then proceed to use some sort of integrated or external download manager to download the latest (or maybe let the user choose) release from Mozilla's ftp server. Then using 7za, extract the installer to the App\ directory and complete installation. Thus rendering the need to update PortableApps manually, unnecessary.
[Attempt to clarify the topic by mod Tim :/ ]
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WinLibre?
but, sadly, not always.
Sometimes as part of an update a program will change what or where it stores data, both to the c: drive and the registry.
The launcher, therefore, needs to be tested and checked out by the developers every single time, to ensure that private data is kept private, and that the app won't mess with any installed versions. There is simply no way to automate this step, so it would be seriously unwise to simply download and over-install the updated version as you suggest.