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[Element Zero]

Inside of Reapers. They're ships, after all. The game mentions Reapers of different types, from transports to harvesters.

They also start manufacturing new troops, on site, also.

[Ashlag]

Also, if you remember Saren (and Benezia, and whomever else) travel around inside Sovereign quite comfortably all through ME1. Who knows if Reapers have giant open areas they can either convert into troop storage/transport or they are just normally built that way. I would imagine they can change their insides depending on what they are doing. So Sovereign made himself look like a ship internally so that Saren was tricked more easily into thinking he was just a ship (before the whole "you are totally indoctrinated and don't care that I'm a Reaper" thing took over Saren). And similarly the other large Reapers could do similar things if they were going to carry the "foot soldiers".