... I can only think of one reason why the Freespace directory should be write protected on a single-user machine ...
That's the issue though, it's not a single-user machine, it's multi-user, whether just one person is using it or not. It's the old DOS/Win9x mentality, where you, the user, is basically God on that machine. On a modern, multi-user OS, you want to be a normal man, and humble man, and just be allowed to mess around with your tiny corner of the world. It's fine to go play God occasion, but it's not really a job that you want full-time.
In other words, you don't really want to run as a user which has the power to do anything. What you want is full control over your tiny bit of the computer and only switch to an admin user when you need to (to add something new to the system, or remove something). System wide files and config can't be changed by you normally, which means that viruses and nasty little spyware programs have great difficulty messing up your computer. Once you start doing this, and get used to it, it's actually kind of nice.
As WMCoolmon said, Windows is still behind the times on this actually being easy. But on my Linux box for instance, I have $HOME on a separate hard drive. All of my own files go there, and programs and system config to on a drive which I don't have write access to as my normal user. When it's time to upgrade to a new OS version I simply erase everything except for $HOME, and install the new OS. When it starts up for the first time I just setup my username that I used before, and all of my settings are just as I left them. This means that I can download a new version of Linux, reboot the computer and install it, reboot the computer to start running it, and that's all, no extra config, nothing. It takes all of 30 minutes and I've switched to a new OS and am immediately back doing e-mail, web browsing, coding, etc.
As for write protecting the FS directory just for virus protection, surely that's going a bit too far with it. I think at that point, it would become an inconvenience more than anything else. You might as well write protect the profile folder as well if you're that concerned about viruses.
The point is that the FS directory would be write protected by default. You wouldn't change anything regarding that, it's just how the user permissions would be set, when set properly. Protecting the profile folder wouldn't be an issue though, since it shouldn't contain executable files for viruses to infect.
So it's in the interests of crossplatform compatibility to have fs2_open support separate pilotfile directories. Doing the same thing under Windows is simply standardizing the interface.
That makes sense, but why does that imply forcing the game to use separate profile directories?
It can't be selectable by it's very nature. It's all or nothing. But it doesn't really have anything to do with cross-platform support, it has to do with supporting current and future Windows versions. We do it with the Linux and OS X builds because that is simply how it's done. Windows is getting to that point, and is largely there already, so we are just playing catch-up on that side.