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.