Found a way to change the cvar-like options without needing to patch the EXE file, seems it's handled through the INI files inside engine\config\platform\pc & engine\config\base dirs, any INI files inside there should be read by the game AFAIK (at least, debug.ini seemed to work).
(EDIT: I'd advise creating a new INI inside "engine\config\platform\pc" instead of editing any existing INI, otherwise the changes could be overwritten by future updates, or possibly break the updater used by GOG - using the platform\pc dir should let the settings override any other setting too)
INI section is the section name of the setting, then you can add the settings themselves like normal INI entries.
eg. for disabling antialiasing, you can add the following:
[Developer/FeatureToggles]
Antialiasing=0
Would be nice if someone can confirm this works for them too.
(AFAIK people have already started work on tools that can patch these settings in the EXE, but those are just for the boolean on/off settings, hopefully through the INI files we should be able to change the integer/string ones too)