The command line handling as I note above is a really crufty old Unix thing that doesn't make sense now and is confusing and offputting when you get papercuts from it.
Another notable thing that they talk about to an extent is process creation -- the fork/exec model in Linux is basically completely broken in the presence of threads. The number of footguns involved in this process has now grown beyond the ability of a human to understand. The Windows model, while a bit more cumbersome seeming at first, is fully generalizable and very explicit about the handoff of handles between processes.
The file system model I think is mostly a wash -- on the one hand, Window's file locking model means that you can't always delete a file that's open, which can be handy. On the other hand, it means that you can't always delete a file that's open, which can be painful. On Linux, it's possible that trying to support POSIX file system semantics can result in unrecoverable sleeps that are nearly impossible to diagnose or fix.