This doesn't necessarily contradict anything in the main proposal, because I'm not exactly sure what is meant by:

Inserting a <script type="packagemap"> after initial document parsing has no effect.

But just in case...

Allowing the packagemap script tag to optionally be dynamically generated by JavaScript would open up quite a bit of flexibility. I would think that typically, this would happen in the head tag of the opening index.html. If it is done there, would this qualify as being done before the initial document parsing has been done?

Use cases would be

1. Pointing to different builds -- customizing referenced libraries based on browser capabilities. This would allow more modern browsers to benefit from smaller downloads (and earlier real adoption, as libraries won't need to wait for the lowest common denominator browser to support the feature before removing the down level compiling). Doing this on the server would be quite difficult, as it would need to maintain a complex lookup between versions of the browser, and which JavaScript capabilities it natively supports.
2. Different references between dev and production. This could more easily be done by the server, but complicates caching strategies.
3. Auto generating large lists of packages based on some wild card rules (e.g. paper-*).