GATE mark is out of 100 and is the actual mark one scored. Now, since there are 2 sessions this is normalized - based on average mark and marks of top 0.1% in each session.
GATE score (out of 1000) is another normalization technique to ensure same playing field for GATE takers across different years. So, even if you score less but gets a high score, it is better for admissions. Most IITs/IISc consider GATE score and not mark.