Per the
FAQ addition to Rare Rules, the embarked unit cannot shoot as it is considered to have Fallen Back and the effects of the stratagem do not transfer to the unit since it does not impose a restriction on the transport.
Shooting Whilst Embarked on a Transport
Some rules, such as Open-topped, enable units to shoot and make ranged attacks even while embarked within a Transport model. Each time such an embarked unit is selected to shoot, the following rules apply to it:
1. Stratagems cannot be used on that unit in order to affect its attacks, and you cannot use the Command Re-roll Stratagem to affect any dice rolls made for its models’ ranged attacks.
2. Measure distances and draw line of sight from any point on the Transport model when models in that unit make the ranged attacks.
3. If the Transport model made a Normal Move, Advanced, Fell Back or Remained Stationary this turn, embarked units are considered to have done the same when they make ranged attacks.
4. While the Transport model is within Engagement Range of any enemy units, unless the ability that the Transport model has that allows its passengers to shoot whilst embarked states otherwise, then models in embarked units cannot make ranged attacks, except with Pistols.
5. Unless specifically stated otherwise, the embarked unit is not affected by the abilities (including aura abilities) of any other unit, even if that unit is also embarked within the same Transport model.
6. If the unit was under the effects of a rule when it embarked on the Transport model (such as rules bestowed on it during the Command phase, by a psychic power or a Stratagem etc.) those rules do not apply to that unit whilst it is embarked.
7. Any abilities (including Detachment abilities) that models in an embarked unit have, or that their weapons have, continue to apply when they make ranged attacks.
8. If a restriction applies to the Transport model, that same restriction applies to units embarked within it. For example, if the Transport model is not eligible to shoot with because it has Advanced or Fallen Back this turn, its passengers are not eligible to shoot with.
9. If a Transport model is under the effects of a modifier to its ranged attacks (such as a modifier to its hit rolls, wound rolls, etc.) the same modifier applies each time an embarked model makes a ranged attack.