1) I thought that the GFDL was already compatible with
CC-BY-SA 3.0,
since they both required derivative works to be published under the
same license. Is there a specific part where they're incompatible,
or is it just a case that there are ambiguities about compatibility,
and the FDL will be revised to remove all doubt?
Indeed, they require both require new versions to be under the same
license as the original, and GFDL isn't the same as CC-BY-SA 3.0, thus
they are incompatible. In spirit, they're pretty similar, but they
have to exactly the same license (up to version numbers, at least) for
them to be interchangeable.
2) More confusingly, I don't see how you can just
"update" a license
and retroactively apply it to all existing content that had been
published under an existing license. All the contributors to
Wikipedia, for example, agreed to the terms of the old FDL when they
submitted their work. How can the updated FDL be said to apply to
that work if the authors didn't agree to it?
Things published on Wikipedia are released under "GFDL v1.2 or later",
so the idea is to make a new version of GFDL which is compatible with
CC-BY-SA.