I am with O-Sora on this one. I really hate Japanese taxis. The drivers are clueless and 100% dependent on GPS, and they annoy me when I am driving. They are also mostly driving around empty. Lower the prices and you might get some customers! I am digressing....
The few times I have taken a taxi with luggage from around Shibuya station then they will just pop the trunk. I am pretty sure 100% of the time. Also when I get to my house they just pop the trunk.
It could be different if they are at an official cab rank. I am hailing them off the street. Upon arrival there is no such excuse.
p.s. O-sora, as a native, will they listen to you if you give them exact turn by turn instructions? I do it in Japanese, but figure that they don't trust me as a gaijin. Instead they will fiddle with their GPS for 5 minutes. Only once did he follow my instructions; the GPS does not necessarily give the best route.