A lot of these issues also stem from the fact that Apple insists on continuing their use of HFS+ as the default file system of OS X. I remember back in the Leopard (10.5) days the rumour was, leading up to WWDC, that Apple was going to announce a move to ZFS as their default file system of choice and that Leopard would be the first release where this was the case. It never happened (apparently licensing issues with Sun (now Oracle) derailed the whole project), but remnants of the initial porting work were still in the OS X command line tools (zpool, etc) for a version or two. Apple totally ported other best-in-breed Solaris tech to OS X (dtrace being a good example) so why ZFS didn't make the cut baffles me given how much utility it would offer.
ZFS basically implements "Time Machine" by default in that you can just say "zfs snapshot" and it creates a read-only snapshot of your file system that uses no additional space until you start making changes / deleting files. You can then copy these snapshots to other physical volumes, or just keep them in place if you want to have a "restore to old version" style functionality.
Time Machine as we know it implements everything that was just native / built in to ZFS by using a series of full copies and hard symlinks and all sorts of kludgy, hacky silliness. It's no wonder it regularly explodes and requires full rebuilding.
Incidentally, I was able to solve my problem (above) by:
1) Disable Time Machine.
2) Stopping all Spotlight indexes (mdutil -d -a).
3) Destroying all Spotlight indexes (rm -rf /.Spotlight-V100) manually.
4) Repairing a file system permission issue with Spotlight (removed a bunch of folders owned by a non-existant user in a /private/var/folders subfolder that Spotlight created). No idea how they got there but they were there and the logs were complaining about them causing a fatal error.
5) Re-enabling Spotlight indexes and letting them build fully.
6) Re-running an initial Time Machine backup.
So, Time Machine is dependent on Spotlight and Spotlight breaks easily. Hence, Time Machine breaks easily. Not a great design.