I've created a little script that can fix / convert the chests in broken worlds:
https://gist.github.com/Gargaj/2891b8fc558e01b8ddf2
(The chests might end up facing the wrong way.)
I haven't tried fixing doors but I'm assuming it's the same datavalue issue, so the fix would pretty much be the same as well.
Seems to be, yes - I searched through JIRA and couldn't find anything related, but I guess I looked for the wrong keywords. We later encountered the door-half-missing problem mentioned in that thread as well.
Either way the repro steps I provided with an actual map download should help.
Tyler: It's a C# program that's built on https://github.com/jaquadro/Substrate