Umm, yes they do. With option 1, if an app isn't running, it isn't consuming memory, meaning more apps can run in the available memory. With option 2, the app isn't present, thus it isn't consuming memory, meaning more apps can run in the available memory. Option 3 is like option 2, except you're doing it on the computer.
Now, if you're looking to decrease the size of the /system partition and give the available space to the /data partition so you can install more apps, forget it. There are very few people I am aware of who can manage such a feat. Not to mention it's impossible to do without sources. Android 3.2 was never released under an open-source license, therefore neither Google nor the manufacturers were required to release their sources.