Good questions. So, if the Titan (and by extension its passengers) are within Synapse then the passengers should be able to be given an order as normal. If the Hierophant goes outside Synapse range the passengers follow their instinctive orders, and if these are Rampage or Hunt they pop out. Whether the Titan loses 5cm of movement is a bit sticky too, and a unit with Nest would indeed get stuck inside.
I would however guess that unlike most transports the Hierophant can effectively "spit 'em out" whenever she feels like it.
A unit with instinctive orders would not be able to mount a transport as that option is not mentioned in the Instinctive behaviour descriptions. (and is kinda disturbing a thought
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