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pg. 55- "Bloodswarm nanoscarabs: At the start of the first game turn, randomly choose one non-vehicle unit in the enemy army. This unit is infested with bloodswarm nanoscarabs- any Flayed One packs entering play via Deep Strike do not scatter if they aim to arrive within 6" of this unit."

If the randomly chosen unit is in a transport, does the Flayed One pack use the transport as the point to where they can deepstrike without scattering?

pg. 55- "Staff of the Destroyer: When firing the Staff of the Destroyer, nominate a direction. Then roll 2D6 and extend a straight line from Imotekh's base in the chosen direction, a distance equal to the total rolled."

Can Imotekh use this weapon when embarked on an open-topped vehicle. Does the vehicle hull count as his base?

Both these questions deal with rules involving transports, of which I do not have good knowledge of precedent rulings involving units embarked on transports.

Yes, as per p66

Yes, as per p66 and open topped rules.