From which Apple store? If it's your local store of course they have VAT built in.
Interesting about amazon japan, never tried it. Have you tried amazon us?
Edit: interesting, amazon.co.jp seems to be its own thing. My login works on amazon US and all european country sites, but it doesn't work on the JP site.
Same situation, If I buy something from aloexpress I also never had to worry about VAT and the duty office. It's somehow handled in the background.
From some amount I assume I'd have to go to the post office and fill in find paperwork, but I never had to for the cheap junk I get from Ali.
Amazon is pretty good at handling VAT and all the import paperwork if it's sold as "Fulfilled by Amazon", regardless if it's the local Amazon site, or the US or Japan sites. I've ordered from all 3.
Even eBay has sorted this out now for orders from the US, with VAT and import fees baked into shipping costs. They give sellers the address for their warehouse in Chicago. eBay then forwards as the seller of record.