If it goes in the safe holstered, there's a good chance the holster will come out with the gun. Removing it with your other hand will slow you down and is likely to cross the hand.
I would personally keep it fully loaded, with one in the chamber. Having to access the safe is slowing you down already. Which gun you put in there will depend on the size of the interior of the safe, and the size of your hand. Practice with the unloaded pistol and see which "draws cleaner" from the safe.
Spare magazines in that small space may get in the way of a safe draw. Since the magazines are relatively harmless by themselves, you might want to leave them elsewhere.
Best of luck,