Oh, these .tsv files are to be related with the surfaces coordinates system, not to the MRI?
That explains why none of what we both tried to do made sense.... I'm going to look into how to apply the same transformation as for the FreeSurfer surfaces in order to create the Brainstorm templates.
Note that storage solution you chose won't be compatible with FreeSurfer or BIDS. For that, the .tsv files should relate either to the coordinates system defined in the reference MRI (scanner coordinates), or to standard spaces (eg. MNI152).