The draft FAQ addresses this:
"Q: I have a question regarding unit special rules that affect all or some units within a certain range of a model or unit. How do these interact with units inside Transports, and what happens if the unit with the rule is inside a Transport?
A: When a unit embarks on a vehicle it is taken off the battlefield and does not interact with anything on the battlefield. However, certain rules may create exceptions to this rule, with the most obvious examples being Fire Points, psychic powers and Transports. If a unit’s rules are meant to apply even when embarked on a Transport, they will specify this."
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