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Boot Camping with a 3rd partition (I know it's non-standard) for data sharing/ease of reinstallations, and possibly to keep applications too… Options are exFAT or NTFS-3G. I went with exFAT originally because it's native and I'd rather not rely on 3rd party drivers for my critical files. However now I'm wondering if I'll run into any issues down the road with regard to permissions, since exFAT doesn't support POSIX ACL—and neither does NTFS; it has its own similar thing, but the advanced [I'm assuming unstable] NTFS-3G add-on can supposedly map between the two. Is that a better bet? If I do ls -al in Terminal on the exFAT drive I get Mac owners, groups, etc., but I don't know where any of those are coming from. What's the best way to go on this?

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When using a non UNIX file system, the permissions you see are default for all files, unless the filesystem logic (i.e. the driver) contains some "translation" from the actual filesystem to those permissions seen by VFS (the filesystem abstraction layer in UNIX and OS X/iOS).

Using a non HFS+ filesystem, and non UFS, will lose the permissions, but not just that - you will also not get filesystem notifications when the filesystem is close to full. Some advanced system calls (like exchangedata(2) ) will not work, either. For the most part, however, most apps don't use these features, so you should be ok. Another issue to consider is case sensitivity - HFS+ isn't (though HFSX is). Using a case sensitive fs may lead to weird results where case insensitivity is assumed, and vice versa.

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