You can choose that coordinate system you want to save in. We have not exposed this on the GUI, as we want to encourage everybody to consistently use LPS coordinate system in all files (as in DICOM, and as it has been always done for images, transforms, etc).
If for a legacy project you want to change what coordinate system is used, you can change the coordinate system for all newly created markups fiducial nodes that are saved in fcsv format, by adding this code snippet to your application startup script:
defaultFiducialStorageNode = slicer.vtkMRMLMarkupsFiducialStorageNode()
Coordinate system choice is preserved if you load and save a node, so you only need to switch the coordinate system for a node once. Even if you load and save the node on another Slicer instance where the startup file was not modified, the coordinate system will still be still RAS.
In case you ever need to change coordinate system in a node to RAS that has been already saved as
LPS then you can run this:
fiducialNode = getNode('F')