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The aerial drop rule from the Scion entry, although a lot of deep strikers use similar wording:

Aerial Drop: During deployment, you can set up this unit in a high-altitude transport, ready to deploy via grav-chute, instead of placing it on the battlefield.

Does this take up a spot in the alternating deployment method? Or is it separate to this sequence? My opinion is that the "instead of" and "during deployment" wording means that it takes up a choice when deploying units.

Yes, it's pretty clear you're setting up a unit, just not on the table.

One exception to this that I can find is that you have to set up an embarked unit at the same time you set up the transport, so you lose a "drop" there.