And for the first one, I thought it might be the key point but I didn't find a really good solution to fix it yet. As it mentioned in the tutorials, it's really hard to indicate those points with a MRI view. So do you have any suggestions also for the coordinates of these anatomical points in MRI vies as the example gave below? https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MRI_coordinates
You are supposed to place the fiducial points NAS/LPA/RPA in the MRI using the same convention that you used for the MEG acquisition. Only you can decide where this points are supposed to be.
I think it is useless to spend too much time trying to find the perferct points: if you are using an anatomy template, this registration is necessarily wrong anyway...
If you had access to more digitized head points, you could warp the template anatomy to match the shape and size of your patient:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping
To keep in mind for your following acquisitions...