I would like an Android build system procedure, command line or Eclipse, to generate several .apk files from a single source codebase. Some common reasons for this - having
Despite your insistence that this is not about packaging shared code into Android libraries, it sort of is. You've stated that markets may have different requirements or having a free and a paid version. In each of these examples, your two final output APKs have different behavior and/or resources. You can put the vast majority of your code in a shared Android library, and then maintain the differences in your actual projects.
For example, I've worked on apps where they need to be released both to the Android Market and the Amazon AppStore. The Amazon AppStore requires that if you link to a market page for the app, it must be Amazon's (as opposed to the Android Market page). You can store a URL in a resource in the library and use that in your code, but then override that resource in the Amazon project to point to the appropriate Amazon URL.
If you structure it right, you can do similar things in code because your starting point is your Application object which you can subclass and do different things with.
That said, if you want to add an Ant step that changes the package name in the manifest, it is just XML. It shouldn't be hard to modify as a precompilation step.