So I've definitely got the right conf file.
I forget which game it is now, but IIRC, Galaxy wasn't using the .conf
files in the game directory. Instead it was using ones, with the same name, under some Galaxy directory.
Well I did a search through my computer but I couldn't find any other folder that might contain separate conf files. However I'm 99% certain Galaxy uses the conf files in the game's folder, because I can change settings for other DOSBox games like Syndicate Plus in those conf files, and when I run the games through Galaxy the changes are properly implemented.
I got a response from GOG support that suggests that Syndicate Wars is a special case DOSBox game where they made a custom DOSBox executable that locks the conf settings. They suggested trying the Windows port but the setup process for that is rather confusing, and there are also reports that there are speed problems with that version too.
So I think I'm out of luck with this game.