If I capture a transport full of fighters and troops etc.

I'm curious about this too, I've never done much of the capturing thing.

since troops and fighters are just load of the transporter i would say you just can use them.
i also think they´ll loose all special skills of the other race.
think of it as captureing a transporter with tanks and fighters but no personal.
if your people use that stuff then they have your own social/racial skills.

So far every time I've capped a ship with cargo I got the cargo. However, the cases mentioned would be unlikely to occur. Especially the "immediate use" part.

Fighters are launched immediately, and I've never seen them return to rearm/refuel. So the odds of capping a ship with fighters on board are slim, unless it's a human-designed semi-carrier (hybrid) with limited launch capacity.

Capping an enemy troop transport would be difficult, and catching a loaded troop transport above an enemy planet? Well, that's going to be so improbable one might as well call it impossible.

Capturing freighters with people works great though.