All carried units disembark, only the largest fights vs the assaulting unit. The disembarking unit does not have a chance to reaction fire.
“… the passengers will automatically dismount and prepare to fight, regardless of any order already given them or their vehicle.” – note there is no suggestion of it only being the unit that will fight in close quarters, just “the passengers”.
Next sentence:
“They may not make any other reaction to the charge.” – this rules out them using reaction fire as that would be making another reaction to the charge.
The next sentence after that is the one that mentions the actual resolution of close quarters being against one of the units dismounting, followed by “If the vehicle is transporting more than one unit, all units on board must dismount, and the largest unit will fight in the assault.”
There is an FAQ which covers your last question – the end up with a Down order:
“I have a query regarding what exactly happens to a unit on a transport if it is assaulted, I know they dismount but…how? How does the unit dismount? Where do you place them? What happens if they win the assault? Can they act if the owning units player gets the next order dice?
The units in the assaulted transport follow the rules for units that are ‘forced to dismount’ from a transport – so they are placed D6″ away from the transport as per regrouping, and then go/remain Down. The assaulting unit is then considered in assault range, regardless of where the troops are placed – simply move the closest assaulting model to the closest dismounted model that is fighting and then continue as per a normal assault.
Note that the dismounting unit can only benefit from the advantages of defending cover if the assaulting unit had to cross cover to reach the transport vehicle in the original assault move against the transport.”
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