IANAXE*, so I may be saying something stupid here, but...
Wouldn't it be possible to come up with a DTD that makes it possible to
tag all the different parts of a draft or an RFC to enable all the
automated processing we love so much, but in such a way that when all
the <.*> sequences are removed, the document in current RFC format
emerges?
This wouldn't lead to authoritativeness problems, and it should allow
taking a draft or RFC and covert it back to an editable document
without making the draft/RFC itself irresistibly editable. And it
doesn't make any assumptions about the format of RFCs, so it shouldn't
be a problem to bring older RFCs under this regime.
* I am not an XML expert