GRT for Discourse overrides quite a few of the base CSS variables in Discourse, but it also includes many of its own variables as well.
It works with the core Discourse CSS wherever possible, and then it adds its own overrides where necessary.
There is not a 1:1 correspondence with everything, though, as the Discourse base makes some assumptions that are incompatible with various aspects of Golden Ratio Typography.
For example, GRT yields 6 usable font sizes (f1–f6), and those are deployed using GRT for Discourse variables (–grt-size-1, --grt-size-2, etc), NOT the base Discourse variables.