Despite having the Silent Wanderer for a long time, Lex had never actually spent much time in it. He had familiarized himself with it, sure, but that included nothing more than a simple tour. He also did not know how to pilot it yet, although it was certainly on his agenda. Cirk, however, had piloted it in both simulations and in real life, although in person he did nothing more than simple systems checks.
Although compared to other ships the silent wanderer was tiny, in reality it was quite big. It had four-bed rooms, a kitchen, a large storage area, a main hall and a cockpit where only two pilots could enter. If they decided to cramp people inside, up to 30 people could fit inside the Wanderer but any more would be problematic. This was also why he made preparations to send the soldiers back via teleportation rather than taking them back through his ship.