Author here. This was actually something that puzzled me too. There must have been many steps between "Want to carry my coffee with me" and "Let's stuff it in a can" that I wasn't clear about. So I did some more digging (but didn't put this in the post because I thought it'd make it very long).

I don't have the definitive answer, but a few things to consider:

- The bottles might have been resealable, but you would have to be worried about leaks for as long as you had the bottle with you. FWIW, the bottles from that time looked like this: https://www.townnews.co.jp/0607/images/a001046055_01.jpg

- Someone going on a long-distance train might not be able to bring the bottle back to the same station

- The store at a different station might not take the bottle from you since shops usually pay a bottle deposit to their suppliers and own the (fungible) bottle

- In many countries with bottled drinks the store charges you a bottle deposit that's much more expensive than the drink. Perhaps the frugal CEO did not want to pay that.

- Or even if he wanted to, did not have the time for that transaction given the train started pulling away