I have a PI installed into a subdirectory (exclusive for all astronomical applications), and it works perfectly.
That's the key concept: give the user freedom to install anywhere. PI just works on any directory you install it (provided you have the required permissions to write on it), and that's true on any supported platform. One of my goals with PI is being as OS-agnostic as possible.
For development purposes, I frankly prefer C:\PCL instead of "C:\Program Files\PCL". One of the reasons is that PixInsight is not a program, it's much more than a program (it provides source code, headers, binary files, documentation, etc.), so putting it into a "Program Files" thing is inaccurate to say the least. And spreading its contents across a web of system folders is, in my opinion, a poorer choice. So why not just PCL, anywhere?