I think any attempt to move this to the "right" location will backfire. There are so many best practices and traditions which different apps/platforms use. for example:
/etc/openacs.tcl seems logical for a single app on a machine
/etc/openacs/appname.tcl seems logical if you have more than one instance on a machine.
/usr/local/aolserver/nsd.tcl is the default for aolserver
/web/appname/config/nsd.tcl is a common tradition
/data/servers/appname/config/ is also common in my company.
The list goes on, there's no way to please everyone so putting it in /files with instructions and letting people put it where they like makes sense to me. Bottom line is it really doesn't matter where it lives, as long as the path is given as as arg to the nsd binary.