I believe the issue with this is that users already largely don't understand decorations in the URL. For example, the difference between a lock and an extended verification certificate bubble. Educating a user on what a bundle URL means technically may be exceedingly challenging.
It seems to me, a lot of the security concerns come from the requirements to make pages served live and pages served from bundles indistinguishable to a user - a requirement that really only makes sense if you're Google and want to make people trust your AMP cache more.
I'd be excited about an alternative proposal for bundles that explicitly distinguishes bundle use in the URL (and also uses a unique origin for all files of the bundle).