You might not think it is important that you are close, but a spouse jam packed onto a Japanese commuter train might think differently.

I haven't been in Japan for a while, so the only thing that comes to mind is Roppongi. Because it is an expat enclave, apartments there are larger, and more expensive.

Apartment sizes are specified as a number and DK, meaning the number of rooms plus the dining and kitchen area. They always have, as far as I know, only one bathroom, which will be separate from the room for the toilet. Rooms are specified in mat sizes, as in a 6-mat room, referring to the number of tatami. Maybe that only applies to traditional apartments, but I don't remember it that way.

I wouldn't worry about being able to make suggestions of areas. Be more concerned about what you want in an apartment and know where you are willing to compromise.

Will the company lease the apartment and sublet it to you, and if not will they pick up the substantial up-front expenses?