Unfortunately, there's not currently a way to configure AtoM's export to include links to the reference display copy instead of the master digital object at the moment. If your institution might be interested in sponsoring the development of a setting to allow for this, please contact me off-list.
In the meantime, here is a workaround that might help:
In most cases, you can access the reference display copy by adding _141 at the end of the URL, just before the file extension. See this previous forum thread for more information:
So, while it's not ideal, you could open your XML files in a text editor, and use the find and replace options to add this (for example, search for .jpg and replace it with _141.jpg throughout the EAD XML file. Repeat as needed for other file formats).
Keep in mind that, if you were importing this XML file into a different AtoM instance, then it will end up using the reference display copy of the digital object from the source system as the master digital object in the target system - so you'll be getting a much lower quality master!
Another option might be to temporarily remove the permissions restriction from accessing the master digital object when importing into your target system. You can do this by modifying the "View master" permissions for the anonymous group, under the Archival description permissions tab. See: