Murray didn't play the Semi final the day before the final. Conditions weren't the same for both.
A 90 minute gentle warmup against someone who offers no threat like Ferrer hardly matters. Djokovic would use more energy in practice normally.
Murray actually had much more taken out of him - he had 4 hours the previous round against Berdych, 3hrs vs Cilic, and 4hrs vs Lopez. Djokovic had walkovers against Lorenzi and Dutra, same against an injured Benneteau, then Wawrinka retired. Only even slightly tricky one was 3hrs vs Del Potro.