[kelnos]

> What I expect it also means is that you'll get inconsistencies when doing inter-process communication, since they'll be using different libraries with potential mismatches. Is this correct?

Only if the libraries that use IPC have changed their wire format between versions, which would be a pretty bad practice, so I wouldn't expect that to happen often (if ever).

If something that's already running has its data files moved around or changed sufficiently, and it later tries to open (that is, the app was running but the data file wasn't open when the upgrade happened) what it thinks is an old data file, but is either new and different or just missing, that could cause problems.

> Because it seems to me that the Windows method might be less flexible but is likely to be more stable, since there's a single coherent global view of the file system at any given time.

In practice I've never had an issue with this (nearly 20 years using various Linux desktop and server distros). Upgrade-in-place is generally the norm, and most people will only reboot if there's a kernel update or an update to the init system.