Sorry it took me so long to see this -- that little "1" next to "My Messages" just doesn't grab my attention very easily. I'll answer your questions as best I can:
1. What is the current status of MC and bookmarking on Podcasts and Audiobooks on iPods (including Nano 3gen, Touch, Classic, and iPhone 2G)?
On my iPod Classic and my 5th gen iPod Video, Podcasts and Audible audiobooks both bookmark automatically (i.e. you don't need to set the "Use Bookmarking" option in MC.)
For non-Audible audiobooks (i.e. mp3 audiobooks ripped from CD or downloaded from other sources), I can get bookmarking to work by setting the "Use Bookmarking" option to "Yes" for these files. I could also get it to work by setting the media type for these files to "Audiobook" but I do NOT do this because I CAN'T STAND the way the iPod classic dumps all audiobooks into a single folder. I prefer to use a GENRE called "audiobooks" instead, and leave the "media sub-type" field blank. This allows me to browse the books by author (i.e. artist) and title, which is a VASTLY (and I mean VASTLY) more convenient way to browse audiobooks. I select the "audiobook" genre, then select an author, then a book. The files for this book (on longer books that use multiple files) play one after the other until they're done, and playback stops. This does not happen with the iPods "audiobooks" category.
Unfortunately, Apple, in their infinite wisdom, changed the way the iPod classic works (and I assume the iPhone works the same way) so that audible books NEVER appear in the normal list of audio tranks -- i.e. they ONLY show up under the iPods "Audiobooks" category, which means that your stuck with ALL the books being dumped into one gigantic folder (which I hate, hate, HATE!!!) This is not an issue on the 5th gen iPod Video, where aa files show up in my normal "genre" list as well. There have been complaints about this on the Apple forums for several years now, but Apple has decided that they know better then iPod users who actually LISTEN to a lot of audiobooks, and have hundreds of "periodical" type aa files on their iPods at one time.
2. With my "generic" workaround (described in the thread linked above), is there anything I need to or can do to get it working?
I started reading over your explanation, but I started getting a bit confused since I'm not that familiar with some of the things your trying. I can say that I don't even try to use both iTunes and MC to sync my iPods for the very reason that you already discovered -- it's a pain in the butt. I just use MC, and I live with any limitations that might cause -- i.e. if MC can't get the iPod to do what I want without iTunes, I just tell myself that the iPod can't do it. Frankly, I can't stand iTunes.
3. All my Podcasts show up in the Music section of my iPod, rather than the Podcast section (and auto-bookmarking doesn't work). Anything I can do here?
Ironically, I WANT both Podcasts and Audiobooks to be listed under their own genres with the rest of the music. I'm actually not clear why people have a problem with this. I just use two genres called "Audiobooks" and "Podcasts" for these files. For people that want to prevent Podcasts and Audiobooks from coming up when shuffling, they simply need to create a smartlist that ignores these two genres and sync it along with the rest of their tracks. By selecting this playlist on the iPod and letting it shuffle, they'll never have a Podcast or Audiobook come up.
Note that the "Podcast" category on the iPod lists the tracks in ASCENDING order, so that when one finishes, the next one in the list is the PREVIOUS one and not the next newer one. In my opinion, the Podcast category on the iPod is nearly as annoying as the "all-in-one-giant-folder" problem with Audiobooks. The iPod's "Podcast" category does have the advantage of "unmarking" the ones you've played, but it has one less level of hierarchy (no "artist" field), and puts them in what many people (like myself) consider a "backwards" order.
I hope this helps somewhat.
Larry
PS. On a related side note, aa chapter points still do not function with MC syncs. They worked with MC 10 and 11 (i.e. "next" and "previous" could take you to chapter points), but as far as I can remember this feature never worked with MC 12 syncs.