I dunno, I've made notes (for what they're worth) on a fair few scripts myself that people have sent me and it's as easy as marking the notes in a nice bold red font in Word, saving it, then sending it back to them. No reams of paper used, no ink, and most importantly it's all conveniently-saved on my PC.
If you make notes in pen on a hard copy, that's it. One copy, no backup, easily-lost. I fail to see why the Writer's Room can't just make notes on submitted scripts on their computers. It's quicker, easier, cheaper, more environmentally-sound, and easier to catalogue and track.