12m2 is not an untypical 10,000yen single room. (often semi-double bed).

The bed takes up 2.5m2. I would guess that the space by the door, the desk and the bathroom each consume 2m2. That leaves 3.5m2 of "gaps" in which you can place your suitcase and walk around the bed.

The thing is, those photos are soooo deceptive. I swear that they must remove a wall to take those shots.

Nikkei Trendy magazine did a ranking a couple of years ago of rooms in the 10,000yen range. Top ranked villa fontaine actually offers 20m2
http://www.jttk.zaq.ne.jp/baaoi603/hotels/tokyo.html

At the "rock bottom" of the range. Some hotels in Osaka offer rooms without bathroom at 2100yen per person. Size = 3 tatami mats. (4.6m2)