Why Amazon japan has a cheaper price gunpla than the gundam base tokyo?
-Probably because of the novelty of getting it there. Like buying merchandise at DisneyWorld compared to getting it online from Amazon or something similar.-
Shipping defeats the purpose
As you know Amazon is a big retailer. And we can say they are first hand supplier. Just imagine the one-way flow and the only cost when products are sent directly from the manufacturer to them. And we all know retailers buy these products from Amazon to re-sell to the other customers. Here for simple: You cannot put too expensive price because you need to sell them again to 2nd or 3rd customers.
If you buy things from Gundam Base. It much more is a prestige and self-happiness only. It's like you visited a famous tourist destination, bought some merchandise from that place, returned home with a pack with Gundam Base Logo, wasnt that a good thing to do?
The last, the Gundam Base visitors are the-end-customers. So nothing is wrong if they charge you more :)
Not related to your statement above. I'm going to say the Gundam Base is really expensive :) I have some friends sighed of the cafe with some kawaii fancy stuffs cost the whole wallet.
What do you think?