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At the moment I can not check the dedicated transport rules from the rulebook so I have to ask if the following is possible or not. So, can I fill my ghost ark with crypteks from the start of the game? I clearly have to take at least some NW to get a ghost ark, but can I still fill it with crypteks from the start of the game? Or do I have to fill it sith NW squad and disembark those and put the crypteks in after that?

This should likely be in YMDC forum since its a rules question, however to the best of my recollection the unit that purchases the transport may either start in, or out of their transport (in this case the necron warriors). When battle commences a different unit may comandeer the vehicle if empty, but may not start inside a different units vehicle.

The Crypteks may not start the game in the Ghost Ark, but they may embark during turn one.
The Necron Warriors do not have to start the game embarked in the Ghost Ark.