I have mostly made "smaller" tax free purchases ranging from the lowest possible at 5500 JPY to around 100000 JPY maximum. As others mentioned the shops used staple some part of the receipt directly in the passport, then later at the airport I would go to the customs counter and they ripped out those receipts. Recently they just "scan" the passport at the shop and then later at the customs counter you scan the passport again. It has also been unclear to me if I needed to be able to present the items or not, but I was never asked any questions at the customs counter after the passport scan.