Responses
They were only on the yacht for two chapters. Ian took Benjamin with him when he went out on his yacht to dispose of Andreas. If you look at the chapter before this one, it says that the yacht incident was several days ago
Look. Sometimes when reading something like this, you just have to... mentally correct the things that don't make sense.
"The Basement" has apparently been in the hold of a boat (probably a super yacht) this entire time. We don't know how many rooms there are but there's at least a dining area, a bedroom, and a couple of office spaces. There's also a decently sized BDSM dungeon with similar equipment scattered around Ian's various work spaces. This is fine. Nothing unusual here.
Benjamin appears to suck as an agent because he's better at fighting than sneaking around. He also got trained by a small group within the CBI since he was young (after his parent's deaths) which is really sus. Any time he does something incredibly stupid, I remind myself: It's not his fault. He grew up in a cult and doesn't know better.
I'm considering the storyline as a 'how I met your mother' and that various things in the retelling have been exaggerated. Ian does not have a third arm as a dick. Benjamin was properly lubricated off screen before taking anything up his ass. It's also possible that just like Ian appears to be super strong, Benjamin is super stretchy there.