I will look into it, but these positions have been validated for every subjects (blue are electrodes, red are fiducial points):
These electrodes are already matched to the heads in the MRI Neurodevelopmental Database, which has been validate at many occasions. They have been further adjusted to the surfaces (slight adjustments on the order of 1-2 mm if I remember well so that they are optimally fit to the meshes) and then they have been re-validated by visualizing them as in the figure above. The image above is generated by importing meshes (separate ones for the head surfaces and the montages) in Blender, so if these were unaligned we would see it directly (I trust much more blender rendering of meshes than neuroimaging software since often neuroimaging works under some assumptions and apply transforms without this being always perfectly clear to the users... whereas blender just plots the 3D coordinated of the vertices and that's it). So the error is probably somewhere between the export function and the plotting in BS. This image is from the templates downloaded from the Git repo? I can download these (scalp surface and montage) and plot them with a meshing software (as barebone as possible) to check that these indeed fit if you'd like.