It isn't great, but I thought the problem was a lot worse than this. I'll look into removing what that file changes from the listenserver.cfg. If anyone adds it directly into listenserver.cfg then it'll stop working, but at least this will help. I am assuming it just gets overridden by listenserver.cfg, rather than ignored entirely.
It gets ignored entirely, this is sorta my fault. Way back when there didnt use to be a listenserver.cfg, at all, and all 'CREATE GAME' information came from the .scr, but that was generating some problems for hosting some public games from my computer via port forwarding. So I noticed there was no listenserver.cfg and added one, and now it seems it broke the use of the settings from the create server menu. So basically someone back in the day knew they couldn't have their create server menu working unless they didnt have a listenserver, then I came around and added a listenserver.cfg and broke it.
I can't figure out anything codeside on how to fix it, but if you type "lservercfgfile settings.scr" into the console, then it'll properly read from the create server dialog box.
I swear to god I've changed about 5 different files referencing to old version name but it just refuses to disappear. It's hiding, somewhere.