I've been running a dual-boot MDD for a very long time. I had constant mysterious directory-related problems early on. However, I never once had a problem - as far as I could tell - with 9 writing something to X. (Of course, I never allowed 9 to attempt to rebuild the X desktop or some such folly)
On the other hand, I had constant recurring problems on my 9 drive until I set the preferences in OSX to keep both Time Machine and Spotlight from caring about - and therefore writing to - the 9 drive. I haven't had any issues since.
I'm well aware there are those well-informed folks on this forum (you know who you are) who absolutely insist that operating a dual-boot Mac is the guaranteed path to cyber hell and damnation, but evidently I'm either blessed or damn lucky or the solution is simple: just treat the two systems as though they're Shiites and Sunnis - don't let them talk to each other and peace will prevail…
Since essentially: volumes = partitions = volumes, I would think it would work the same way on a single partitioned drive. Am I missing something?