When importing the anatomy folder, Brainstorm converts everything to its own coordinate systems, described the tutorial you reference, no matter from what program it was generated.
Surface coordinates are always saved in SCS coordinates in Brainstorm.
if we want to plot electrodes in the pial, we need Surface RAS coordinates
Plot in which environment?
The conversion you need to do depends mainly on the software in which you want to import your coordinates.
Please give some more background on what you are currently trying to do, and describe exactly where and how you are stuck.