The current implementation is pretty basic - if the logo provided is oversized, then yes, Imagemagick (the tool we use for image processing) will just arbitrarily crop the content. Please see:
From the note on uploading logos found on that page:
AtoM requires that the image uploaded as the institution logo be in PNG format. The image cannot exceed 256k in size. If the image selected for upload does not meet these requirements, you will receive an error message below the “Logo” field after clicking the “Save” button, and your upload will not be saved.
Ideally, the image size should be between 200x200 and 270x270 pixels square. If the image you upload does not meet these sizing specifications, it will be automatically cropped by ImageMagick to meet the requirements listed above.
Note that the in-page help in AtoM's user interface also says that the image will be cropped if too big:
This could certainly be improved in the future, but would likely require development sponsorship or community code contribution. For more information on how we maintain and develop AtoM, please see:
In the meantime, you should make use of external tools to prepare the logo as you want it prior to uploading.