My feeling is that the subtitles should reflect the original authenticity as much as possible. Basically, this script is being used as a "raw material" for people's own purposes. So, if you think the subs should be in the black bars and outside of overscan, you should take the script and edit it to display that way. But the starting point should be theatrical authenticity, which people can then modify for their own preferences.
I guess people who don't have the knowledge to edit the script will kind of get the shaft. But the alternative is shafting everyone not on CRTs, and non-CRTs are the majority now.
I guess this is in reference mainly to Gforce's script, since DJ could edit his how he sees fit. But I am always for theatrical authenticity.